6-153605318-C-T

Position:

• chr6-153605318-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 0.244 in 152,092 control chromosomes in the GnomAD database, including 6,098 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 0.24 (6098 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.463 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: 0.244 AC: 37031 AN: 151974 Hom.: 6093 Cov.: 32

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.0139

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.244 AC: 37059 AN: 152092 Hom.: 6098 Cov.: 32 AF XY: 0.237 AC XY: 17613 AN XY: 74342

Gnomad4 AFR AF: 0.469

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.0139

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.237

Alfa AF: 0.180 Hom.: 5637

Bravo AF: 0.258

Asia WGS AF: 0.0790 AC: 276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.43
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7754521; hg19: chr6-153926453; COSMIC: COSV60293705;