rs10501886

Variant names:

• chr11-98406379-C-T
• rs10501886

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.036 in 152,176 control chromosomes in the GnomAD database, including 128 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 0.036 (128 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.573
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.036 (5475/152176) while in subpopulation AFR AF = 0.0432 (1793/41502). AF 95% confidence interval is 0.0415. There are 128 homozygotes in GnomAd4. There are 2551 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 128 gene

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: 0.0360 AC: 5471 AN: 152058 Hom.: 128 Cov.: 32

Gnomad AFR AF: 0.0432

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0363

Gnomad ASJ AF: 0.0798

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0207

Gnomad FIN AF: 0.00972

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0364

Gnomad OTH AF: 0.0464

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

GnomAD4 genome AF: 0.0360 AC: 5475 AN: 152176 Hom.: 128 Cov.: 32 AF XY: 0.0343 AC XY: 2551 AN XY: 74412

African (AFR) AF: 0.0432 AC: 1793 AN: 41502

American (AMR) AF: 0.0363 AC: 554 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0798 AC: 277 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.0207 AC: 100 AN: 4822

European-Finnish (FIN) AF: 0.00972 AC: 103 AN: 10600

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0365 AC: 2480 AN: 68012

Other (OTH) AF: 0.0459 AC: 97 AN: 2112

Alfa AF: 0.0352 Hom.: 10

Bravo AF: 0.0393

Asia WGS AF: 0.0110 AC: 37 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.62
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs10501886; hg19: chr11-98277108;