6-79756407-A-G

Position:

• chr6-79756407-A-G

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 0.643 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

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 (AFR) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

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: 0.643 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

Gnomad4 AFR AF: 0.839

Gnomad4 AMR AF: 0.612

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.558

Gnomad4 SAS AF: 0.689

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.552

Gnomad4 OTH AF: 0.614

Alfa AF: 0.557 Hom.: 34644

Bravo AF: 0.645

Asia WGS AF: 0.665 AC: 2311 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	2.2
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6925255; hg19: chr6-80466124;