rs726488

Variant names:

• chr6-99091317-C-T
• rs726488

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 0.782 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

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 (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

Gnomad4 AFR AF: 0.775

Gnomad4 AMR AF: 0.743

Gnomad4 ASJ AF: 0.748

Gnomad4 EAS AF: 0.651

Gnomad4 SAS AF: 0.746

Gnomad4 FIN AF: 0.757

Gnomad4 NFE AF: 0.811

Gnomad4 OTH AF: 0.787

Alfa AF: 0.753 Hom.: 4548

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs726488; hg19: chr6-99539193;