6-5952358-C-T

Position:

• chr6-5952358-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 0.608 in 152,000 control chromosomes in the GnomAD database, including 28,510 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 0.61 (28510 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

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 = 0.708 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92324 AN: 151880 Hom.: 28497 Cov.: 32

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.608 AC: 92392 AN: 152000 Hom.: 28510 Cov.: 32 AF XY: 0.601 AC XY: 44621 AN XY: 74306

Gnomad4 AFR AF: 0.715

Gnomad4 AMR AF: 0.567

Gnomad4 ASJ AF: 0.584

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.505

Gnomad4 FIN AF: 0.544

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.599

Alfa AF: 0.589 Hom.: 11982

Bravo AF: 0.616

Asia WGS AF: 0.505 AC: 1758 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	0.071
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4960147; hg19: chr6-5952591;