dbSNP rs2099077: ENSG00000296261:n.36-3854C>A (chr5-103428347-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 ENST00000737662.1(ENSG00000296261):n.36-3854C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,100 control chromosomes in the GnomAD database, including 2,777 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 0.16 ( 2777 hom., cov: 32)

Consequence

ENSG00000296261
ENST00000737662.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.450

Publications

6 publications found

Variant links:

Genes affected

ENSG00000296261 (HGNC:):

ENSG00000296261 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=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000296261	ENST00000737662.1 link	n.36-3854C>A	intron_variant	Intron 1 of 1
ENSG00000296261	ENST00000737663.1 link	n.430-3854C>A	intron_variant	Intron 1 of 1
ENSG00000293393	ENST00000737782.1 link	n.716+4141G>T	intron_variant	Intron 6 of 7

Frequencies

GnomAD3 genomes

AF:

0.164

AC:

24888

AN:

151982

Hom.:

2760

Cov.:

show subpopulations

Gnomad AFR

AF:

0.297

Gnomad AMI

AF:

0.152

Gnomad AMR

AF:

0.209

Gnomad ASJ

AF:

0.142

Gnomad EAS

AF:

0.182

Gnomad SAS

AF:

0.176

Gnomad FIN

AF:

0.0652

Gnomad MID

AF:

0.152

Gnomad NFE

AF:

0.0876

Gnomad OTH

AF:

0.148

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

GnomAD4 genome

AF:

0.164

AC:

24946

AN:

152100

Hom.:

2777

Cov.:

AF XY:

0.164

AC XY:

12176

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.297

AC:

12330

AN:

41446

American (AMR)

AF:

0.209

AC:

3194

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.142

AC:

491

AN:

3466

East Asian (EAS)

AF:

0.182

AC:

944

AN:

5178

South Asian (SAS)

AF:

0.175

AC:

846

AN:

4822

European-Finnish (FIN)

AF:

0.0652

AC:

691

AN:

10598

Middle Eastern (MID)

AF:

0.139

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0875

AC:

5953

AN:

68006

Other (OTH)

AF:

0.150

AC:

317

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1009

2018

3028

4037

5046

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

248

496

744

992

1240

<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:

0.120

Hom.:

2458

Bravo

AF:

0.177

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.79

(source)

DANN

Benign

0.44

PhyloP100

-0.45

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