rs10512441

Variant names:

• chr17-32912627-C-T
• rs10512441

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;