6-61253680-C-T

Position:

• chr6-61253680-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 0.832 in 152,068 control chromosomes in the GnomAD database, including 52,940 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 0.83 (52940 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.709

Genes affected

(HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.61253680C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.832 AC: 126489 AN: 151950 Hom.: 52901 Cov.: 33

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.816

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.819

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

GnomAD4 genome AF: 0.832 AC: 126583 AN: 152068 Hom.: 52940 Cov.: 33 AF XY: 0.827 AC XY: 61445 AN XY: 74294

Gnomad4 AFR AF: 0.779

Gnomad4 AMR AF: 0.816

Gnomad4 ASJ AF: 0.788

Gnomad4 EAS AF: 0.705

Gnomad4 SAS AF: 0.778

Gnomad4 FIN AF: 0.866

Gnomad4 NFE AF: 0.880

Gnomad4 OTH AF: 0.817

Alfa AF: 0.863 Hom.: 9651

Bravo AF: 0.827

Asia WGS AF: 0.726 AC: 2525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.29
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs840061; hg19: chr6-61984034;