rs10500664

Positions:

• chr11-6664327-G-A
• chr11-6664327-G-C
• chr11-6664327-G-T

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 0.849 in 152,040 control chromosomes in the GnomAD database, including 55,694 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 0.85 (55694 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.

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: 0.849 AC: 129046 AN: 151924 Hom.: 55652 Cov.: 30

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.909

Gnomad ASJ AF: 0.913

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.949

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.908

Gnomad OTH AF: 0.871

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

GnomAD4 genome AF: 0.849 AC: 129145 AN: 152040 Hom.: 55694 Cov.: 30 AF XY: 0.852 AC XY: 63329 AN XY: 74344

Gnomad4 AFR AF: 0.687

Gnomad4 AMR AF: 0.909

Gnomad4 ASJ AF: 0.913

Gnomad4 EAS AF: 0.987

Gnomad4 SAS AF: 0.781

Gnomad4 FIN AF: 0.949

Gnomad4 NFE AF: 0.908

Gnomad4 OTH AF: 0.872

Alfa AF: 0.886 Hom.: 28094

Bravo AF: 0.841

Asia WGS AF: 0.847 AC: 2946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.5
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10500664; hg19: chr11-6685558;