Genetic Variant NM_006288.5:c.374-139G>A (chr11-119419659-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006288.5(THY1):c.374-139G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 665,294 control chromosomes in the GnomAD database, including 22,993 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.24 ( 4874 hom., cov: 33)

Exomes 𝑓: 0.26 ( 18119 hom. )

Consequence

THY1
NM_006288.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.352

Publications

2 publications found

Variant links:

Genes affected

THY1 (HGNC:11801): (Thy-1 cell surface antigen) This gene encodes a cell surface glycoprotein and member of the immunoglobulin superfamily of proteins. The encoded protein is involved in cell adhesion and cell communication in numerous cell types, but particularly in cells of the immune and nervous systems. The encoded protein is widely used as a marker for hematopoietic stem cells. This gene may function as a tumor suppressor in nasopharyngeal carcinoma. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2015]

THY1 links:

USP2-AS1 (HGNC:48673): (USP2 antisense RNA 1)

USP2-AS1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006288.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
THY1	NM_006288.5	MANE Select	c.374-139G>A	intron	N/A	NP_006279.2
THY1	NM_001311160.2		c.374-139G>A	intron	N/A	NP_001298089.1	P04216
THY1	NM_001311162.2		c.374-139G>A	intron	N/A	NP_001298091.1	P04216

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
THY1	ENST00000284240.10	TSL:1 MANE Select	c.374-139G>A	intron	N/A	ENSP00000284240.6	P04216
THY1	ENST00000918469.1		c.530-139G>A	intron	N/A	ENSP00000588528.1
THY1	ENST00000900759.1		c.410-139G>A	intron	N/A	ENSP00000570818.1

Frequencies

GnomAD3 genomes

AF:

0.240

AC:

36482

AN:

152066

Hom.:

4874

Cov.:

show subpopulations

Gnomad AFR

AF:

0.137

Gnomad AMI

AF:

0.211

Gnomad AMR

AF:

0.313

Gnomad ASJ

AF:

0.276

Gnomad EAS

AF:

0.0865

Gnomad SAS

AF:

0.114

Gnomad FIN

AF:

0.286

Gnomad MID

AF:

0.215

Gnomad NFE

AF:

0.297

Gnomad OTH

AF:

0.257

GnomAD4 exome

AF:

0.256

AC:

131456

AN:

513110

Hom.:

18119

Cov.:

AF XY:

0.249

AC XY:

67337

AN XY:

270000

show subpopulations

African (AFR)

AF:

0.135

AC:

1884

AN:

13996

American (AMR)

AF:

0.308

AC:

6831

AN:

22188

Ashkenazi Jewish (ASJ)

AF:

0.279

AC:

4025

AN:

14438

East Asian (EAS)

AF:

0.113

AC:

3665

AN:

32466

South Asian (SAS)

AF:

0.115

AC:

5668

AN:

49364

European-Finnish (FIN)

AF:

0.286

AC:

12976

AN:

45426

Middle Eastern (MID)

AF:

0.216

AC:

451

AN:

2084

European-Non Finnish (NFE)

AF:

0.291

AC:

88802

AN:

305098

Other (OTH)

AF:

0.255

AC:

7154

AN:

28050

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

4859

9718

14578

19437

24296

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

648

1296

1944

2592

3240

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.240

AC:

36490

AN:

152184

Hom.:

4874

Cov.:

AF XY:

0.235

AC XY:

17512

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.137

AC:

5699

AN:

41524

American (AMR)

AF:

0.313

AC:

4779

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.276

AC:

959

AN:

3472

East Asian (EAS)

AF:

0.0867

AC:

449

AN:

5178

South Asian (SAS)

AF:

0.114

AC:

551

AN:

4830

European-Finnish (FIN)

AF:

0.286

AC:

3035

AN:

10594

Middle Eastern (MID)

AF:

0.218

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.297

AC:

20224

AN:

67986

Other (OTH)

AF:

0.255

AC:

538

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1417

2834

4252

5669

7086

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

374

748

1122

1496

1870

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.275

Hom.:

2058

Bravo

AF:

0.239

Asia WGS

AF:

0.114

AC:

399

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.0

(source)

DANN

Benign

0.38

PhyloP100

-0.35

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over