6-153942144-T-C

Variant names:

• chr6-153942144-T-C
• rs282096

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;