dbSNP rs10501162: ENSG00000306379:n.284+14398C>A (chr11-36725205-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000817320.1(ENSG00000306379):n.284+14398C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,144 control chromosomes in the GnomAD database, including 2,438 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 0.17 ( 2438 hom., cov: 32)

Consequence

ENSG00000306379
ENST00000817320.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.260

Publications

4 publications found

Variant links:

Genes affected

ENSG00000306379 (HGNC:):

ENSG00000306379 links:

Genome browser will be placed here

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=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984326	XR_001748187.1 link	n.576+14398C>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306379	ENST00000817320.1 link	n.284+14398C>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.170

AC:

25891

AN:

152026

Hom.:

2439

Cov.:

show subpopulations

Gnomad AFR

AF:

0.231

Gnomad AMI

AF:

0.136

Gnomad AMR

AF:

0.130

Gnomad ASJ

AF:

0.123

Gnomad EAS

AF:

0.163

Gnomad SAS

AF:

0.111

Gnomad FIN

AF:

0.163

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.152

Gnomad OTH

AF:

0.156

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

GnomAD4 genome

AF:

0.170

AC:

25904

AN:

152144

Hom.:

2438

Cov.:

AF XY:

0.170

AC XY:

12620

AN XY:

74390

show subpopulations

African (AFR)

AF:

0.231

AC:

9573

AN:

41482

American (AMR)

AF:

0.130

AC:

1981

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.123

AC:

428

AN:

3472

East Asian (EAS)

AF:

0.162

AC:

838

AN:

5166

South Asian (SAS)

AF:

0.111

AC:

534

AN:

4822

European-Finnish (FIN)

AF:

0.163

AC:

1725

AN:

10600

Middle Eastern (MID)

AF:

0.109

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.152

AC:

10340

AN:

67998

Other (OTH)

AF:

0.156

AC:

329

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1085

2170

3256

4341

5426

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

266

532

798

1064

1330

<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:

0.157

Hom.:

350

Bravo

AF:

0.171

Asia WGS

AF:

0.163

AC:

566

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.9

(source)

DANN

Benign

0.53

PhyloP100

-0.26

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