rs1281978

chr6-153152097-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 0.571 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;