6-79756407-A-G

Variant names:

• chr6-79756407-A-G
• rs6925255

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 0.643 in 152,108 control chromosomes in the GnomAD database, including 32,818 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 0.64 (32818 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170
• Publications: 3 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 (AFR) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97739 AN: 151990 Hom.: 32764 Cov.: 33

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.643 AC: 97854 AN: 152108 Hom.: 32818 Cov.: 33 AF XY: 0.646 AC XY: 48073 AN XY: 74364

African (AFR) AF: 0.839 AC: 34849 AN: 41528

American (AMR) AF: 0.612 AC: 9352 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1443 AN: 3464

East Asian (EAS) AF: 0.558 AC: 2884 AN: 5170

South Asian (SAS) AF: 0.689 AC: 3322 AN: 4820

European-Finnish (FIN) AF: 0.610 AC: 6448 AN: 10562

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.552 AC: 37513 AN: 67966

Other (OTH) AF: 0.614 AC: 1295 AN: 2110

Alfa AF: 0.580 Hom.: 69473

Bravo AF: 0.645

Asia WGS AF: 0.665 AC: 2311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.50
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs6925255; hg19: chr6-80466124;