rs10501767

Variant names:

• chr11-91936990-C-T
• rs10501767

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 0.208 in 152,032 control chromosomes in the GnomAD database, including 3,443 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 (3443 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.23 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: 0.208 AC: 31596 AN: 151914 Hom.: 3448 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.0901

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.208 AC: 31606 AN: 152032 Hom.: 3443 Cov.: 32 AF XY: 0.206 AC XY: 15321 AN XY: 74314

African (AFR) AF: 0.171 AC: 7087 AN: 41496

American (AMR) AF: 0.175 AC: 2664 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 923 AN: 3468

East Asian (EAS) AF: 0.200 AC: 1035 AN: 5174

South Asian (SAS) AF: 0.220 AC: 1058 AN: 4820

European-Finnish (FIN) AF: 0.227 AC: 2395 AN: 10570

Middle Eastern (MID) AF: 0.360 AC: 105 AN: 292

European-Non Finnish (NFE) AF: 0.233 AC: 15836 AN: 67938

Other (OTH) AF: 0.199 AC: 421 AN: 2112

Alfa AF: 0.216 Hom.: 1695

Bravo AF: 0.203

Asia WGS AF: 0.171 AC: 595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.5
DANN	Benign	0.65
PhyloP100		-0.041

Splicing

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

Other links and lift over

dbSNP: rs10501767; hg19: chr11-91670156;