rs2688610

Variant names:

• chr10-73895173-G-A
• rs2688610

Your query was ambiguous. Multiple possible variants found:

• chr10-73895173-G-A
• chr10-73895173-G-C
• chr10-73895173-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 0.436 in 151,712 control chromosomes in the GnomAD database, including 16,014 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 0.44 (16014 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.567
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66191 AN: 151602 Hom.: 16008 Cov.: 31

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.436 AC: 66211 AN: 151712 Hom.: 16014 Cov.: 31 AF XY: 0.431 AC XY: 31914 AN XY: 74104

African (AFR) AF: 0.263 AC: 10859 AN: 41348

American (AMR) AF: 0.431 AC: 6565 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1975 AN: 3468

East Asian (EAS) AF: 0.110 AC: 568 AN: 5176

South Asian (SAS) AF: 0.329 AC: 1582 AN: 4810

European-Finnish (FIN) AF: 0.472 AC: 4939 AN: 10456

Middle Eastern (MID) AF: 0.596 AC: 174 AN: 292

European-Non Finnish (NFE) AF: 0.559 AC: 37994 AN: 67912

Other (OTH) AF: 0.508 AC: 1071 AN: 2110

Alfa AF: 0.516 Hom.: 81006

Bravo AF: 0.426

Asia WGS AF: 0.212 AC: 737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.27
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs2688610; hg19: chr10-75654931;