dbSNP rs2160847: ENSG00000296241:n.435+793T>C (chr2-210736392-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000737540.1(ENSG00000296241):n.435+793T>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 152,160 control chromosomes in the GnomAD database, including 2,821 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 ( 2821 hom., cov: 32)

Consequence

ENSG00000296241
ENST00000737540.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.55

Publications

5 publications found

Variant links:

Genes affected

ENSG00000296241 (HGNC:):

ENSG00000296241 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=-1.01).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.215 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
ENSG00000296241	ENST00000737540.1 link	n.435+793T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.183

AC:

27885

AN:

152042

Hom.:

2816

Cov.:

show subpopulations

Gnomad AFR

AF:

0.105

Gnomad AMI

AF:

0.198

Gnomad AMR

AF:

0.221

Gnomad ASJ

AF:

0.195

Gnomad EAS

AF:

0.154

Gnomad SAS

AF:

0.208

Gnomad FIN

AF:

0.321

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.202

Gnomad OTH

AF:

0.176

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

GnomAD4 genome

AF:

0.183

AC:

27901

AN:

152160

Hom.:

2821

Cov.:

AF XY:

0.189

AC XY:

14039

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.105

AC:

4341

AN:

41528

American (AMR)

AF:

0.221

AC:

3378

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.195

AC:

677

AN:

3470

East Asian (EAS)

AF:

0.155

AC:

801

AN:

5178

South Asian (SAS)

AF:

0.210

AC:

1010

AN:

4818

European-Finnish (FIN)

AF:

0.321

AC:

3399

AN:

10588

Middle Eastern (MID)

AF:

0.105

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.202

AC:

13714

AN:

67984

Other (OTH)

AF:

0.175

AC:

369

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1151

2302

3452

4603

5754

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

314

628

942

1256

1570

<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:

0.191

Hom.:

647

Bravo

AF:

0.172

Asia WGS

AF:

0.174

AC:

609

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.36

(source)

DANN

Benign

0.47

PhyloP100

-2.5

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