6-79844864-G-T

Position:

• chr6-79844864-G-T

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 0.14 in 152,084 control chromosomes in the GnomAD database, including 1,920 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 0.14 (1920 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.414 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: 0.140 AC: 21324 AN: 151964 Hom.: 1915 Cov.: 30

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.0966

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0924

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.140 AC: 21358 AN: 152084 Hom.: 1920 Cov.: 30 AF XY: 0.144 AC XY: 10679 AN XY: 74360

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.428

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.0966

Gnomad4 NFE AF: 0.0924

Gnomad4 OTH AF: 0.131

Alfa AF: 0.103 Hom.: 392

Bravo AF: 0.149

Asia WGS AF: 0.320 AC: 1110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.4
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs719172; hg19: chr6-80554581;