rs276699

Variant names:

• chr6-75746331-G-C
• rs276699

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 0.0877 in 152,152 control chromosomes in the GnomAD database, including 777 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 0.088 (777 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.238
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.281 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: 0.0877 AC: 13329 AN: 152034 Hom.: 777 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0769

Gnomad ASJ AF: 0.0378

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0839

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0607

Gnomad OTH AF: 0.0948

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

GnomAD4 genome AF: 0.0877 AC: 13339 AN: 152152 Hom.: 777 Cov.: 32 AF XY: 0.0888 AC XY: 6603 AN XY: 74388

African (AFR) AF: 0.114 AC: 4746 AN: 41516

American (AMR) AF: 0.0767 AC: 1171 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0378 AC: 131 AN: 3470

East Asian (EAS) AF: 0.294 AC: 1518 AN: 5170

South Asian (SAS) AF: 0.111 AC: 533 AN: 4818

European-Finnish (FIN) AF: 0.0839 AC: 888 AN: 10590

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0607 AC: 4125 AN: 68000

Other (OTH) AF: 0.0953 AC: 201 AN: 2110

Alfa AF: 0.0710 Hom.: 57

Bravo AF: 0.0903

Asia WGS AF: 0.190 AC: 658 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.61
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs276699; hg19: chr6-76456048;