rs682664

Variant names:

• chr10-127833298-G-A
• rs682664

Your query was ambiguous. Multiple possible variants found:

• chr10-127833298-G-A
• chr10-127833298-G-C
• chr10-127833298-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.519 in 152,062 control chromosomes in the GnomAD database, including 21,827 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 0.52 (21827 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.477
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.598 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: 0.519 AC: 78924 AN: 151944 Hom.: 21812 Cov.: 33

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.519 AC: 78976 AN: 152062 Hom.: 21827 Cov.: 33 AF XY: 0.525 AC XY: 39029 AN XY: 74324

African (AFR) AF: 0.314 AC: 13029 AN: 41462

American (AMR) AF: 0.573 AC: 8757 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1865 AN: 3472

East Asian (EAS) AF: 0.616 AC: 3179 AN: 5164

South Asian (SAS) AF: 0.509 AC: 2459 AN: 4830

European-Finnish (FIN) AF: 0.668 AC: 7044 AN: 10542

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.599 AC: 40723 AN: 67996

Other (OTH) AF: 0.538 AC: 1134 AN: 2108

Alfa AF: 0.554 Hom.: 3686

Bravo AF: 0.505

Asia WGS AF: 0.585 AC: 2036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.2
DANN	Benign	0.52
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs682664; hg19: chr10-129631562;