6-88555187-G-T

Variant names:

• chr6-88555187-G-T
• rs2610715

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 0.637 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.653 AC: 27032 AN: 41390

American (AMR) AF: 0.567 AC: 8654 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 2136 AN: 3468

East Asian (EAS) AF: 0.509 AC: 2619 AN: 5148

South Asian (SAS) AF: 0.560 AC: 2701 AN: 4820

European-Finnish (FIN) AF: 0.705 AC: 7450 AN: 10560

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.650 AC: 44166 AN: 67954

Other (OTH) AF: 0.630 AC: 1331 AN: 2112

Alfa AF: 0.633 Hom.: 10690

Bravo AF: 0.624

Asia WGS AF: 0.519 AC: 1805 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.38
PhyloP100		0.026

Splicing

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

Other links and lift over

dbSNP: rs2610715; hg19: chr6-89264906;