rs11191666

Variant names:

• chr10-103367521-A-G
• rs11191666

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 0.406 in 151,516 control chromosomes in the GnomAD database, including 13,281 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 0.41 (13281 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.358

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.623 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: 0.406 AC: 61516 AN: 151396 Hom.: 13278 Cov.: 29

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.406 AC: 61544 AN: 151516 Hom.: 13281 Cov.: 29 AF XY: 0.411 AC XY: 30457 AN XY: 74018

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.434

Gnomad4 SAS AF: 0.642

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.454

Gnomad4 OTH AF: 0.408

Alfa AF: 0.454 Hom.: 21937

Bravo AF: 0.391

Asia WGS AF: 0.514 AC: 1784 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	4.2
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11191666; hg19: chr10-105127278;