dbSNP rs4937523: ENSG00000301321:n.93+507G>T (chr11-130477295-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000777947.1(ENSG00000301321):n.93+507G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 152,044 control chromosomes in the GnomAD database, including 11,807 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 0.38 ( 11807 hom., cov: 32)

Consequence

ENSG00000301321
ENST00000777947.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0970

Publications

5 publications found

Variant links:

Genes affected

ENSG00000301321 (HGNC:):

ENSG00000301321 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000301321	ENST00000777947.1 link	n.93+507G>T	intron_variant	Intron 1 of 3
ENSG00000301321	ENST00000777948.1 link	n.303+268G>T	intron_variant	Intron 1 of 3
ENSG00000301321	ENST00000777949.1 link	n.236+268G>T	intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.384

AC:

58333

AN:

151926

Hom.:

11787

Cov.:

show subpopulations

Gnomad AFR

AF:

0.508

Gnomad AMI

AF:

0.360

Gnomad AMR

AF:

0.357

Gnomad ASJ

AF:

0.350

Gnomad EAS

AF:

0.482

Gnomad SAS

AF:

0.419

Gnomad FIN

AF:

0.361

Gnomad MID

AF:

0.399

Gnomad NFE

AF:

0.310

Gnomad OTH

AF:

0.384

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

GnomAD4 genome

AF:

0.384

AC:

58402

AN:

152044

Hom.:

11807

Cov.:

AF XY:

0.387

AC XY:

28749

AN XY:

74300

show subpopulations

African (AFR)

AF:

0.509

AC:

21087

AN:

41454

American (AMR)

AF:

0.357

AC:

5452

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.350

AC:

1214

AN:

3470

East Asian (EAS)

AF:

0.481

AC:

2478

AN:

5148

South Asian (SAS)

AF:

0.418

AC:

2014

AN:

4820

European-Finnish (FIN)

AF:

0.361

AC:

3817

AN:

10570

Middle Eastern (MID)

AF:

0.384

AC:

113

AN:

294

European-Non Finnish (NFE)

AF:

0.310

AC:

21085

AN:

67980

Other (OTH)

AF:

0.386

AC:

814

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1808

3617

5425

7234

9042

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

554

1108

1662

2216

2770

<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:

0.337

Hom.:

37877

Bravo

AF:

0.389

Asia WGS

AF:

0.451

AC:

1563

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.8

(source)

DANN

Benign

0.55

PhyloP100

-0.097

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