rs10197940

chr2-151397404-T-Cchr2-151397404-T-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.465

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.409

Alfa AF: 0.419 Hom.: 26894

Bravo AF: 0.402

Asia WGS AF: 0.521 AC: 1812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.71
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10197940; hg19: chr2-152253918;