dbSNP rs1207731: ENSG00000296253:n.161-646A>C (chr7-97020044-A-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000737644.1(ENSG00000296253):n.161-646A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,092 control chromosomes in the GnomAD database, including 2,692 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 0.18 ( 2692 hom., cov: 32)

Consequence

ENSG00000296253
ENST00000737644.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.609

Publications

5 publications found

Variant links:

Genes affected

ENSG00000296253 (HGNC:):

ENSG00000296253 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.42).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.208 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
ENSG00000296253	ENST00000737644.1 link	n.161-646A>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.183

AC:

27782

AN:

151974

Hom.:

2691

Cov.:

show subpopulations

Gnomad AFR

AF:

0.171

Gnomad AMI

AF:

0.240

Gnomad AMR

AF:

0.166

Gnomad ASJ

AF:

0.122

Gnomad EAS

AF:

0.145

Gnomad SAS

AF:

0.142

Gnomad FIN

AF:

0.123

Gnomad MID

AF:

0.196

Gnomad NFE

AF:

0.211

Gnomad OTH

AF:

0.181

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

GnomAD4 genome

AF:

0.183

AC:

27798

AN:

152092

Hom.:

2692

Cov.:

AF XY:

0.177

AC XY:

13130

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.171

AC:

7084

AN:

41480

American (AMR)

AF:

0.166

AC:

2531

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.122

AC:

424

AN:

3470

East Asian (EAS)

AF:

0.145

AC:

749

AN:

5174

South Asian (SAS)

AF:

0.144

AC:

692

AN:

4820

European-Finnish (FIN)

AF:

0.123

AC:

1297

AN:

10584

Middle Eastern (MID)

AF:

0.201

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.211

AC:

14364

AN:

67958

Other (OTH)

AF:

0.179

AC:

379

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1184

2368

3551

4735

5919

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

304

608

912

1216

1520

<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:

0.202

Hom.:

13801

Bravo

AF:

0.185

Asia WGS

AF:

0.136

AC:

471

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.42

CADD

Benign

(source)

DANN

Benign

0.82

PhyloP100

0.61

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