6-153962074-C-T

Variant names:

• chr6-153962074-C-T
• rs647303

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 0.801 in 151,294 control chromosomes in the GnomAD database, including 48,849 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 0.80 (48849 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.801 AC: 121043 AN: 151176 Hom.: 48823 Cov.: 27

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.833

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.826

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.785

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

GnomAD4 genome AF: 0.801 AC: 121117 AN: 151294 Hom.: 48849 Cov.: 27 AF XY: 0.803 AC XY: 59327 AN XY: 73854

Gnomad4 AFR AF: 0.890

Gnomad4 AMR AF: 0.833

Gnomad4 ASJ AF: 0.671

Gnomad4 EAS AF: 0.757

Gnomad4 SAS AF: 0.790

Gnomad4 FIN AF: 0.826

Gnomad4 NFE AF: 0.746

Gnomad4 OTH AF: 0.779

Alfa AF: 0.753 Hom.: 21204

Bravo AF: 0.805

Asia WGS AF: 0.756 AC: 2621 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.8
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs647303; hg19: chr6-154283209;