6-78675752-C-T

Position:

• chr6-78675752-C-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 0.793 in 152,100 control chromosomes in the GnomAD database, including 48,012 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 0.79 (48012 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.856 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: 0.793 AC: 120515 AN: 151982 Hom.: 47967 Cov.: 32

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.931

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.858

Gnomad EAS AF: 0.842

Gnomad SAS AF: 0.879

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.822

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.793 AC: 120621 AN: 152100 Hom.: 48012 Cov.: 32 AF XY: 0.790 AC XY: 58750 AN XY: 74364

Gnomad4 AFR AF: 0.810

Gnomad4 AMR AF: 0.790

Gnomad4 ASJ AF: 0.858

Gnomad4 EAS AF: 0.843

Gnomad4 SAS AF: 0.878

Gnomad4 FIN AF: 0.716

Gnomad4 NFE AF: 0.781

Gnomad4 OTH AF: 0.787

Alfa AF: 0.781 Hom.: 9185

Bravo AF: 0.798

Asia WGS AF: 0.867 AC: 3016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1938551; hg19: chr6-79385469;