rs10197940

Variant names:

• chr2-151397404-T-C
• rs10197940

Your query was ambiguous. Multiple possible variants found:

• chr2-151397404-T-C
• chr2-151397404-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.408 in 152,000 control chromosomes in the GnomAD database, including 12,692 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 0.41 (12692 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.86
• Publications: 22 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.408 AC: 62034 AN: 151880 Hom.: 12673 Cov.: 32

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.408 AC: 62080 AN: 152000 Hom.: 12692 Cov.: 32 AF XY: 0.408 AC XY: 30324 AN XY: 74316

African (AFR) AF: 0.360 AC: 14934 AN: 41480

American (AMR) AF: 0.391 AC: 5960 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1265 AN: 3462

East Asian (EAS) AF: 0.469 AC: 2420 AN: 5164

South Asian (SAS) AF: 0.465 AC: 2240 AN: 4818

European-Finnish (FIN) AF: 0.414 AC: 4375 AN: 10562

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.436 AC: 29603 AN: 67962

Other (OTH) AF: 0.409 AC: 862 AN: 2110

Alfa AF: 0.421 Hom.: 56777

Bravo AF: 0.402

Asia WGS AF: 0.521 AC: 1812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.71
DANN	Benign	0.39
PhyloP100		-2.9

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10197940; hg19: chr2-152253918;