rs10510642

Variant names:

• chr3-30919096-T-C
• rs10510642

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 0.15 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.498 AC: 20626 AN: 41422

American (AMR) AF: 0.0558 AC: 853 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00691 AC: 24 AN: 3472

East Asian (EAS) AF: 0.103 AC: 531 AN: 5180

South Asian (SAS) AF: 0.0461 AC: 222 AN: 4820

European-Finnish (FIN) AF: 0.00273 AC: 29 AN: 10624

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.00312 AC: 212 AN: 68030

Other (OTH) AF: 0.113 AC: 238 AN: 2108

Alfa AF: 0.0626 Hom.: 2690

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
PhyloP100		-0.0070

Splicing

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

Other links and lift over

dbSNP: rs10510642; hg19: chr3-30960588;