rs10199388

Variant names:

• chr2-240674832-G-A
• rs10199388

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 0.805 in 151,242 control chromosomes in the GnomAD database, including 49,109 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 0.80 (49109 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.836 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

Frequencies

GnomAD3 genomes AF: 0.805 AC: 121607 AN: 151128 Hom.: 49069 Cov.: 31

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.809

Gnomad AMR AF: 0.848

Gnomad ASJ AF: 0.818

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.914

Gnomad NFE AF: 0.805

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.805 AC: 121690 AN: 151242 Hom.: 49109 Cov.: 31 AF XY: 0.800 AC XY: 59145 AN XY: 73888

Gnomad4 AFR AF: 0.835

Gnomad4 AMR AF: 0.849

Gnomad4 ASJ AF: 0.818

Gnomad4 EAS AF: 0.640

Gnomad4 SAS AF: 0.733

Gnomad4 FIN AF: 0.722

Gnomad4 NFE AF: 0.805

Gnomad4 OTH AF: 0.827

Alfa AF: 0.808 Hom.: 9500

Bravo AF: 0.817

Asia WGS AF: 0.650 AC: 2260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	0.61
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10199388; hg19: chr2-241614249;