1-153067689-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 0.566 in 151,906 control chromosomes in the GnomAD database, including 25,156 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 (25156 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.972

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.711 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: 0.566 AC: 85930 AN: 151788 Hom.: 25117 Cov.: 32

Gnomad AFR AF: 0.718

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.663

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.566 AC: 86026 AN: 151906 Hom.: 25156 Cov.: 32 AF XY: 0.562 AC XY: 41720 AN XY: 74254

Gnomad4 AFR AF: 0.718

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.663

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.508

Gnomad4 OTH AF: 0.545

Alfa AF: 0.519 Hom.: 3474

Bravo AF: 0.577

Asia WGS AF: 0.568 AC: 1977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.96
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs576941; hg19: chr1-153040165;