chr6-79172992-T-C

Position:

• chr6-79172992-T-C

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 0.871 in 152,206 control chromosomes in the GnomAD database, including 59,340 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 0.87 (59340 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.388

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 (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.872 AC: 132567 AN: 152088 Hom.: 59326 Cov.: 32

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.974

Gnomad AMR AF: 0.921

Gnomad ASJ AF: 0.926

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.984

Gnomad FIN AF: 0.957

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.963

Gnomad OTH AF: 0.899

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

GnomAD4 genome AF: 0.871 AC: 132623 AN: 152206 Hom.: 59340 Cov.: 32 AF XY: 0.874 AC XY: 65062 AN XY: 74416

Gnomad4 AFR AF: 0.643

Gnomad4 AMR AF: 0.921

Gnomad4 ASJ AF: 0.926

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.984

Gnomad4 FIN AF: 0.957

Gnomad4 NFE AF: 0.963

Gnomad4 OTH AF: 0.900

Alfa AF: 0.905 Hom.: 10000

Bravo AF: 0.857

Asia WGS AF: 0.954 AC: 3315 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.5
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: rs1360841; hg19: chr6-79882709;