rs6595726

Positions:

• chr5-126680552-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 0.648 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.648 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

Gnomad4 AFR AF: 0.741

Gnomad4 AMR AF: 0.701

Gnomad4 ASJ AF: 0.614

Gnomad4 EAS AF: 0.965

Gnomad4 SAS AF: 0.826

Gnomad4 FIN AF: 0.565

Gnomad4 NFE AF: 0.557

Gnomad4 OTH AF: 0.662

Alfa AF: 0.587 Hom.: 51203

Bravo AF: 0.663

Asia WGS AF: 0.882 AC: 3065 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6595726; hg19: chr5-126016244;