rs10512437

chr17-31695334-G-A

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 0.231 in 151,786 control chromosomes in the GnomAD database, including 4,608 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 0.23 (4608 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.200

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.298 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: 0.231 AC: 35051 AN: 151670 Hom.: 4608 Cov.: 31

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.0970

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.231 AC: 35059 AN: 151786 Hom.: 4608 Cov.: 31 AF XY: 0.228 AC XY: 16887 AN XY: 74136

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.0965

Gnomad4 FIN AF: 0.342

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.248

Alfa AF: 0.268 Hom.: 3311

Bravo AF: 0.217

Asia WGS AF: 0.163 AC: 565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.46
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10512437; hg19: chr17-30022353;