rs2610715

chr6-88555187-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 0.637 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;