rs726488

Variant names:

• chr6-99091317-C-T
• rs726488

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 0.782 in 152,156 control chromosomes in the GnomAD database, including 46,704 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 0.78 (46704 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301
• Publications: 1 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 (NFE) allele frequency at 95% confidence interval = 0.805 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: 0.782 AC: 118905 AN: 152038 Hom.: 46664 Cov.: 33

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.931

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.811

Gnomad OTH AF: 0.790

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

GnomAD4 genome AF: 0.782 AC: 118997 AN: 152156 Hom.: 46704 Cov.: 33 AF XY: 0.778 AC XY: 57891 AN XY: 74382

African (AFR) AF: 0.775 AC: 32182 AN: 41510

American (AMR) AF: 0.743 AC: 11354 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.748 AC: 2597 AN: 3470

East Asian (EAS) AF: 0.651 AC: 3373 AN: 5178

South Asian (SAS) AF: 0.746 AC: 3599 AN: 4822

European-Finnish (FIN) AF: 0.757 AC: 8010 AN: 10578

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.811 AC: 55126 AN: 68000

Other (OTH) AF: 0.787 AC: 1657 AN: 2106

Alfa AF: 0.754 Hom.: 4783

Bravo AF: 0.780

Asia WGS AF: 0.735 AC: 2557 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.42
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs726488; hg19: chr6-99539193;