6-153942144-T-C

Variant names:

• chr6-153942144-T-C
• rs282096

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.515 AC: 21325 AN: 41430

American (AMR) AF: 0.492 AC: 7519 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1876 AN: 3470

East Asian (EAS) AF: 0.439 AC: 2271 AN: 5170

South Asian (SAS) AF: 0.497 AC: 2397 AN: 4822

European-Finnish (FIN) AF: 0.641 AC: 6767 AN: 10556

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.627 AC: 42589 AN: 67964

Other (OTH) AF: 0.567 AC: 1197 AN: 2112

Alfa AF: 0.597 Hom.: 33587

Bravo AF: 0.561

Asia WGS AF: 0.423 AC: 1474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.43
DANN	Benign	0.69
PhyloP100		-1.0

Splicing

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

Other links and lift over

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