chr5-126680552-G-T

Variant names:

• chr5-126680552-G-T
• rs6595726

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 0.648 in 151,976 control chromosomes in the GnomAD database, including 32,904 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 0.65 (32904 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.713
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 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: 0.648 AC: 98447 AN: 151858 Hom.: 32856 Cov.: 32

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.965

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.648 AC: 98547 AN: 151976 Hom.: 32904 Cov.: 32 AF XY: 0.656 AC XY: 48698 AN XY: 74250

African (AFR) AF: 0.741 AC: 30749 AN: 41474

American (AMR) AF: 0.701 AC: 10706 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2129 AN: 3470

East Asian (EAS) AF: 0.965 AC: 4975 AN: 5158

South Asian (SAS) AF: 0.826 AC: 3974 AN: 4812

European-Finnish (FIN) AF: 0.565 AC: 5965 AN: 10558

Middle Eastern (MID) AF: 0.663 AC: 191 AN: 288

European-Non Finnish (NFE) AF: 0.557 AC: 37876 AN: 67940

Other (OTH) AF: 0.662 AC: 1396 AN: 2108

Alfa AF: 0.594 Hom.: 106816

Bravo AF: 0.663

Asia WGS AF: 0.882 AC: 3065 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.23
DANN	Benign	0.62
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs6595726; hg19: chr5-126016244;