rs10510642

Positions:

• chr3-30919096-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 0.15 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;