rs947591

Variant names:

• chr10-92735996-C-A
• rs947591

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 0.388 in 152,078 control chromosomes in the GnomAD database, including 12,335 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 0.39 (12335 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.395
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.465 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: 0.388 AC: 58955 AN: 151960 Hom.: 12334 Cov.: 31

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.388 AC: 58977 AN: 152078 Hom.: 12335 Cov.: 31 AF XY: 0.388 AC XY: 28801 AN XY: 74322

African (AFR) AF: 0.264 AC: 10942 AN: 41476

American (AMR) AF: 0.422 AC: 6453 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1343 AN: 3468

East Asian (EAS) AF: 0.153 AC: 792 AN: 5172

South Asian (SAS) AF: 0.311 AC: 1499 AN: 4814

European-Finnish (FIN) AF: 0.452 AC: 4777 AN: 10574

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.469 AC: 31914 AN: 67986

Other (OTH) AF: 0.411 AC: 866 AN: 2106

Alfa AF: 0.442 Hom.: 24949

Bravo AF: 0.381

Asia WGS AF: 0.267 AC: 928 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	0.12
DANN	Benign	0.34
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs947591; hg19: chr10-94495753;