6-24646593-C-T

Position:

• chr6-24646593-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 0.415 in 152,026 control chromosomes in the GnomAD database, including 13,377 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 0.42 (13377 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.858

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.457 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: 0.415 AC: 63110 AN: 151908 Hom.: 13371 Cov.: 32

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.415 AC: 63139 AN: 152026 Hom.: 13377 Cov.: 32 AF XY: 0.407 AC XY: 30265 AN XY: 74316

Gnomad4 AFR AF: 0.463

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.387

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.409

Alfa AF: 0.430 Hom.: 15674

Bravo AF: 0.419

Asia WGS AF: 0.264 AC: 919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3756821; hg19: chr6-24646821;