rs10501886

chr11-98406379-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 128 gene

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: 0.0360 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

Gnomad4 AFR AF: 0.0432

Gnomad4 AMR AF: 0.0363

Gnomad4 ASJ AF: 0.0798

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0207

Gnomad4 FIN AF: 0.00972

Gnomad4 NFE AF: 0.0365

Gnomad4 OTH AF: 0.0459

Alfa AF: 0.0340 Hom.: 9

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10501886; hg19: chr11-98277108;