rs2610715

Variant names:

• chr6-88555187-G-T
• rs2610715

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 0.637 in 151,926 control chromosomes in the GnomAD database, including 30,953 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 0.64 (30953 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.647 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: 0.637 AC: 96737 AN: 151808 Hom.: 30928 Cov.: 31

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.634

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

GnomAD4 genome AF: 0.637 AC: 96812 AN: 151926 Hom.: 30953 Cov.: 31 AF XY: 0.637 AC XY: 47316 AN XY: 74262

Gnomad4 AFR AF: 0.653

Gnomad4 AMR AF: 0.567

Gnomad4 ASJ AF: 0.616

Gnomad4 EAS AF: 0.509

Gnomad4 SAS AF: 0.560

Gnomad4 FIN AF: 0.705

Gnomad4 NFE AF: 0.650

Gnomad4 OTH AF: 0.630

Alfa AF: 0.647 Hom.: 5892

Bravo AF: 0.624

Asia WGS AF: 0.519 AC: 1805 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2610715; hg19: chr6-89264906;