rs6458065

Positions:

• chr6-38673578-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 0.538 in 151,922 control chromosomes in the GnomAD database, including 22,237 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 0.54 (22237 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.942

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.558 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: 0.538 AC: 81627 AN: 151804 Hom.: 22222 Cov.: 31

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.538 AC: 81687 AN: 151922 Hom.: 22237 Cov.: 31 AF XY: 0.533 AC XY: 39539 AN XY: 74244

Gnomad4 AFR AF: 0.564

Gnomad4 AMR AF: 0.548

Gnomad4 ASJ AF: 0.525

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.559

Gnomad4 OTH AF: 0.499

Alfa AF: 0.548 Hom.: 46791

Bravo AF: 0.542

Asia WGS AF: 0.387 AC: 1343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6458065; hg19: chr6-38641354;