dbSNP rs9327881: ENSG00000296261:n.35+42707G>A (chr5-103389394-G-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.35+42707G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,046 control chromosomes in the GnomAD database, including 1,447 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 0.12 ( 1447 hom., cov: 32)

Consequence

ENSG00000296261
ENST00000737662.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.63

Publications

5 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296261	ENST00000737662.1 link	n.35+42707G>A		intron_variant	Intron 1 of 1
ENSG00000296261	ENST00000737663.1 link	n.429+35155G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.123

AC:

18658

AN:

151928

Hom.:

1445

Cov.:

show subpopulations

Gnomad AFR

AF:

0.222

Gnomad AMI

AF:

0.0877

Gnomad AMR

AF:

0.0725

Gnomad ASJ

AF:

0.0779

Gnomad EAS

AF:

0.103

Gnomad SAS

AF:

0.0587

Gnomad FIN

AF:

0.103

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.0860

Gnomad OTH

AF:

0.110

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

GnomAD4 genome

AF:

0.123

AC:

18676

AN:

152046

Hom.:

1447

Cov.:

AF XY:

0.122

AC XY:

9077

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.222

AC:

9195

AN:

41452

American (AMR)

AF:

0.0727

AC:

1110

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.0779

AC:

270

AN:

3468

East Asian (EAS)

AF:

0.103

AC:

533

AN:

5158

South Asian (SAS)

AF:

0.0589

AC:

284

AN:

4818

European-Finnish (FIN)

AF:

0.103

AC:

1087

AN:

10586

Middle Eastern (MID)

AF:

0.139

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0860

AC:

5844

AN:

67980

Other (OTH)

AF:

0.110

AC:

232

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

802

1603

2405

3206

4008

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

194

388

582

776

970

<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:

0.0997

Hom.:

2442

Bravo

AF:

0.128

Asia WGS

AF:

0.0860

AC:

303

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.026

(source)

DANN

Benign

0.29

PhyloP100

-1.6

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