rs10500664

Variant names:

• chr11-6664327-G-A
• rs10500664

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;