Genetic Variant LOC107984179:n.1967T>C (chr10-44400587-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The XR_001747298.2(LOC107984179):n.1967T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 152,154 control chromosomes in the GnomAD database, including 11,726 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 0.37 ( 11726 hom., cov: 32)

Consequence

LOC107984179
XR_001747298.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.48

Publications

2 publications found

Variant links:

Genes affected

LOC107984179 (HGNC:):

LOC107984179 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=-0.82).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984179	XR_001747298.2 link	n.1967T>C		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303087	ENST00000791650.1 link	n.488-1122T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.369

AC:

56086

AN:

152036

Hom.:

11718

Cov.:

show subpopulations

Gnomad AFR

AF:

0.169

Gnomad AMI

AF:

0.398

Gnomad AMR

AF:

0.499

Gnomad ASJ

AF:

0.440

Gnomad EAS

AF:

0.229

Gnomad SAS

AF:

0.309

Gnomad FIN

AF:

0.443

Gnomad MID

AF:

0.478

Gnomad NFE

AF:

0.459

Gnomad OTH

AF:

0.430

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.369

AC:

56094

AN:

152154

Hom.:

11726

Cov.:

AF XY:

0.370

AC XY:

27531

AN XY:

74386

show subpopulations

African (AFR)

AF:

0.169

AC:

7000

AN:

41520

American (AMR)

AF:

0.499

AC:

7631

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.440

AC:

1528

AN:

3470

East Asian (EAS)

AF:

0.229

AC:

1183

AN:

5174

South Asian (SAS)

AF:

0.308

AC:

1484

AN:

4814

European-Finnish (FIN)

AF:

0.443

AC:

4684

AN:

10584

Middle Eastern (MID)

AF:

0.473

AC:

139

AN:

294

European-Non Finnish (NFE)

AF:

0.459

AC:

31182

AN:

67986

Other (OTH)

AF:

0.426

AC:

900

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1748

3496

5243

6991

8739

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

530

1060

1590

2120

2650

<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:

0.436

Hom.:

24628

Bravo

AF:

0.365

Asia WGS

AF:

0.257

AC:

897

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.70

(source)

DANN

Benign

0.67

PhyloP100

-1.5

Splicing

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over