rs3124199

Positions:

• chr10-30500659-T-C

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 0.61 in 151,866 control chromosomes in the GnomAD database, including 28,967 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 0.61 (28967 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.273

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.746 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: 0.609 AC: 92460 AN: 151748 Hom.: 28914 Cov.: 30

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.610 AC: 92573 AN: 151866 Hom.: 28967 Cov.: 30 AF XY: 0.607 AC XY: 45063 AN XY: 74198

Gnomad4 AFR AF: 0.753

Gnomad4 AMR AF: 0.630

Gnomad4 ASJ AF: 0.526

Gnomad4 EAS AF: 0.520

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.557

Gnomad4 NFE AF: 0.547

Gnomad4 OTH AF: 0.583

Alfa AF: 0.561 Hom.: 32289

Bravo AF: 0.624

Asia WGS AF: 0.533 AC: 1854 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3124199; hg19: chr10-30789588;