chr6-153942144-T-C

Position:

• chr6-153942144-T-C

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 0.57 in 152,004 control chromosomes in the GnomAD database, including 24,905 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 0.57 (24905 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.622 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: 0.570 AC: 86580 AN: 151886 Hom.: 24885 Cov.: 32

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.570 AC: 86634 AN: 152004 Hom.: 24905 Cov.: 32 AF XY: 0.567 AC XY: 42102 AN XY: 74312

Gnomad4 AFR AF: 0.515

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.541

Gnomad4 EAS AF: 0.439

Gnomad4 SAS AF: 0.497

Gnomad4 FIN AF: 0.641

Gnomad4 NFE AF: 0.627

Gnomad4 OTH AF: 0.567

Alfa AF: 0.601 Hom.: 25821

Bravo AF: 0.561

Asia WGS AF: 0.423 AC: 1474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.43
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs282096; hg19: chr6-154263279; COSMIC: COSV68007000;