rs10512441

Positions:

• chr17-32912627-C-T

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 0.211 in 152,130 control chromosomes in the GnomAD database, including 3,597 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 0.21 (3597 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.262 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: 0.211 AC: 32022 AN: 152012 Hom.: 3589 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.00635

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.211 AC: 32060 AN: 152130 Hom.: 3597 Cov.: 32 AF XY: 0.206 AC XY: 15332 AN XY: 74384

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.00636

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.170

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.224

Alfa AF: 0.200 Hom.: 5285

Bravo AF: 0.214

Asia WGS AF: 0.125 AC: 432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	9.2
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10512441; hg19: chr17-31239645;