Genetic Variant LOC105374187:n.10928+3300C>T (chr3-161275076-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 XR_001740993.2(LOC105374187):n.10928+3300C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,036 control chromosomes in the GnomAD database, including 6,813 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 0.29 ( 6813 hom., cov: 33)

Consequence

LOC105374187
XR_001740993.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0820

Publications

22 publications found

Variant links:

Genes affected

LOC105374187 (HGNC:):

LOC105374187 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=-0.79).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105374187	XR_001740993.2 link	n.10928+3300C>T	intron_variant	Intron 2 of 2
LOC105374187	XR_001740994.2 link	n.992+3300C>T	intron_variant	Intron 1 of 2
LOC105374187	XR_007096150.1 link	n.992+3300C>T	intron_variant	Intron 1 of 1
LOC105374187	XR_007096151.1 link	n.10206+5054C>T	intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.286

AC:

43401

AN:

151918

Hom.:

6811

Cov.:

show subpopulations

Gnomad AFR

AF:

0.165

Gnomad AMI

AF:

0.182

Gnomad AMR

AF:

0.364

Gnomad ASJ

AF:

0.357

Gnomad EAS

AF:

0.531

Gnomad SAS

AF:

0.354

Gnomad FIN

AF:

0.311

Gnomad MID

AF:

0.313

Gnomad NFE

AF:

0.312

Gnomad OTH

AF:

0.283

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

GnomAD4 genome

AF:

0.286

AC:

43413

AN:

152036

Hom.:

6813

Cov.:

AF XY:

0.290

AC XY:

21521

AN XY:

74304

show subpopulations

African (AFR)

AF:

0.165

AC:

6832

AN:

41472

American (AMR)

AF:

0.364

AC:

5564

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.357

AC:

1238

AN:

3468

East Asian (EAS)

AF:

0.531

AC:

2745

AN:

5172

South Asian (SAS)

AF:

0.355

AC:

1706

AN:

4810

European-Finnish (FIN)

AF:

0.311

AC:

3283

AN:

10548

Middle Eastern (MID)

AF:

0.320

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.312

AC:

21196

AN:

67976

Other (OTH)

AF:

0.279

AC:

589

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1576

3153

4729

6306

7882

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

470

940

1410

1880

2350

<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:

0.312

Hom.:

2144

Bravo

AF:

0.283

Asia WGS

AF:

0.368

AC:

1278

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

2.0

(source)

DANN

Benign

0.76

PhyloP100

-0.082

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