6-54769237-G-T

Position:

• chr6-54769237-G-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 0.682 in 152,074 control chromosomes in the GnomAD database, including 36,657 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 0.68 (36657 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.354

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 (AFR) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.54769237G>T		intergenic_region
LOC107986606	XR_001744176.3	n.95+32500C>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103618 AN: 151956 Hom.: 36617 Cov.: 32

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.812

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.682 AC: 103703 AN: 152074 Hom.: 36657 Cov.: 32 AF XY: 0.674 AC XY: 50114 AN XY: 74328

Gnomad4 AFR AF: 0.850

Gnomad4 AMR AF: 0.499

Gnomad4 ASJ AF: 0.680

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.655

Gnomad4 FIN AF: 0.598

Gnomad4 NFE AF: 0.662

Gnomad4 OTH AF: 0.655

Alfa AF: 0.671 Hom.: 15761

Bravo AF: 0.676

Asia WGS AF: 0.529 AC: 1843 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	0.45
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1566753; hg19: chr6-54634035;