6-80696852-T-C

Position:

• chr6-80696852-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 0.552 in 151,884 control chromosomes in the GnomAD database, including 24,396 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 0.55 (24396 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83795 AN: 151766 Hom.: 24396 Cov.: 31

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.552 AC: 83819 AN: 151884 Hom.: 24396 Cov.: 31 AF XY: 0.553 AC XY: 41043 AN XY: 74214

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.620

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.723

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.694

Gnomad4 NFE AF: 0.627

Gnomad4 OTH AF: 0.589

Alfa AF: 0.598 Hom.: 5519

Bravo AF: 0.541

Asia WGS AF: 0.583 AC: 2025 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.5
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1377986; hg19: chr6-81406569;