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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.437 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

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.472

Gnomad4 NFE AF: 0.559

Gnomad4 OTH AF: 0.508

Alfa AF: 0.534 Hom.: 36441

Bravo AF: 0.426

Asia WGS AF: 0.212 AC: 737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2688610; hg19: chr10-75654931;