chr6-153152097-C-T

Variant names:

• chr6-153152097-C-T
• rs1281978

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 0.571 in 152,032 control chromosomes in the GnomAD database, including 26,117 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 (26117 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.762 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: 0.571 AC: 86761 AN: 151914 Hom.: 26066 Cov.: 33

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.571 AC: 86865 AN: 152032 Hom.: 26117 Cov.: 33 AF XY: 0.564 AC XY: 41885 AN XY: 74294

Gnomad4 AFR AF: 0.769

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.538

Gnomad4 EAS AF: 0.294

Gnomad4 SAS AF: 0.316

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.515

Gnomad4 OTH AF: 0.564

Alfa AF: 0.536 Hom.: 10946

Bravo AF: 0.584

Asia WGS AF: 0.356 AC: 1240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.098
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1281978; hg19: chr6-153473232; COSMIC: COSV69430557;