6-79844864-G-T

Variant names:

• chr6-79844864-G-T
• rs719172

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;