rs763726

chr6-84883633-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.00757 in 152,242 control chromosomes in the GnomAD database, including 25 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 0.0076 (25 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.32

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00757 (1152/152242) while in subpopulation EAS AF= 0.0533 (275/5162). AF 95% confidence interval is 0.0481. There are 25 homozygotes in gnomad4. There are 657 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 26 gene

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: 0.00757 AC: 1152 AN: 152124 Hom.: 26 Cov.: 33

Gnomad AFR AF: 0.000676

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0477

Gnomad ASJ AF: 0.000576

Gnomad EAS AF: 0.0537

Gnomad SAS AF: 0.00228

Gnomad FIN AF: 0.00453

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000588

Gnomad OTH AF: 0.00767

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

GnomAD4 genome AF: 0.00757 AC: 1152 AN: 152242 Hom.: 25 Cov.: 33 AF XY: 0.00883 AC XY: 657 AN XY: 74428

Gnomad4 AFR AF: 0.000674

Gnomad4 AMR AF: 0.0479

Gnomad4 ASJ AF: 0.000576

Gnomad4 EAS AF: 0.0533

Gnomad4 SAS AF: 0.00228

Gnomad4 FIN AF: 0.00453

Gnomad4 NFE AF: 0.000588

Gnomad4 OTH AF: 0.00759

Alfa AF: 0.00496 Hom.: 2

Bravo AF: 0.0124

Asia WGS AF: 0.0210 AC: 73 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
Cadd	Benign	20
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs763726; hg19: chr6-85593351;