rs2675609

Variant names:

• chr10-61876772-T-C
• rs2675609

Your query was ambiguous. Multiple possible variants found:

• chr10-61876772-T-C
• chr10-61876772-T-G

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 0.608 in 152,056 control chromosomes in the GnomAD database, including 28,278 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 0.61 (28278 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.545

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.648 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: 0.608 AC: 92313 AN: 151938 Hom.: 28256 Cov.: 32

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.608 AC: 92375 AN: 152056 Hom.: 28278 Cov.: 32 AF XY: 0.602 AC XY: 44741 AN XY: 74332

Gnomad4 AFR AF: 0.655

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.609

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.573

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.626

Gnomad4 OTH AF: 0.607

Alfa AF: 0.586 Hom.: 8897

Bravo AF: 0.593

Asia WGS AF: 0.594 AC: 2064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.0
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2675609; hg19: chr10-63636531;