6-85251291-C-T

Position:

• chr6-85251291-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 0.724 in 152,032 control chromosomes in the GnomAD database, including 40,235 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 0.72 (40235 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.10

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.921 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.85251291C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.723 AC: 109906 AN: 151914 Hom.: 40184 Cov.: 32

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.943

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.738

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

GnomAD4 genome AF: 0.724 AC: 110013 AN: 152032 Hom.: 40235 Cov.: 32 AF XY: 0.723 AC XY: 53676 AN XY: 74278

Gnomad4 AFR AF: 0.805

Gnomad4 AMR AF: 0.804

Gnomad4 ASJ AF: 0.704

Gnomad4 EAS AF: 0.943

Gnomad4 SAS AF: 0.628

Gnomad4 FIN AF: 0.616

Gnomad4 NFE AF: 0.664

Gnomad4 OTH AF: 0.736

Alfa AF: 0.694 Hom.: 4587

Bravo AF: 0.746

Asia WGS AF: 0.769 AC: 2673 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	19
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1570108; hg19: chr6-85961009; COSMIC: COSV69410987;