rs10510642

Variant names:

• chr3-30919096-T-C
• rs10510642

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 0.15 in 152,154 control chromosomes in the GnomAD database, including 5,335 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 0.15 (5335 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.492 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: 0.149 AC: 22680 AN: 152038 Hom.: 5308 Cov.: 32

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0559

Gnomad ASJ AF: 0.00691

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.0464

Gnomad FIN AF: 0.00273

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.00312

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.150 AC: 22750 AN: 152154 Hom.: 5335 Cov.: 32 AF XY: 0.147 AC XY: 10917 AN XY: 74400

Gnomad4 AFR AF: 0.498

Gnomad4 AMR AF: 0.0558

Gnomad4 ASJ AF: 0.00691

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.0461

Gnomad4 FIN AF: 0.00273

Gnomad4 NFE AF: 0.00312

Gnomad4 OTH AF: 0.113

Alfa AF: 0.0419 Hom.: 1217

Bravo AF: 0.169

Asia WGS AF: 0.0830 AC: 287 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	3.9
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10510642; hg19: chr3-30960588;