chr6-7712469-C-G

Variant names:

• chr6-7712469-C-G
• rs7769495

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 0.404 in 152,080 control chromosomes in the GnomAD database, including 13,011 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 0.40 (13011 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.497
• Publications: 4 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 (SAS) allele frequency at 95% confidence interval = 0.528 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: 0.404 AC: 61346 AN: 151962 Hom.: 13008 Cov.: 33

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.404 AC: 61377 AN: 152080 Hom.: 13011 Cov.: 33 AF XY: 0.401 AC XY: 29773 AN XY: 74338

African (AFR) AF: 0.297 AC: 12322 AN: 41476

American (AMR) AF: 0.314 AC: 4807 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 1466 AN: 3472

East Asian (EAS) AF: 0.237 AC: 1227 AN: 5172

South Asian (SAS) AF: 0.545 AC: 2630 AN: 4822

European-Finnish (FIN) AF: 0.474 AC: 5006 AN: 10560

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.477 AC: 32448 AN: 67968

Other (OTH) AF: 0.380 AC: 803 AN: 2112

Alfa AF: 0.309 Hom.: 822

Bravo AF: 0.383

Asia WGS AF: 0.347 AC: 1208 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	5.7
DANN	Benign	0.49
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs7769495; hg19: chr6-7712702;