rs4275453

chr1-159738257-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 0.611 in 151,950 control chromosomes in the GnomAD database, including 29,285 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 0.61 (29285 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.303

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.695 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: 0.611 AC: 92789 AN: 151834 Hom.: 29258 Cov.: 31

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.753

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.611 AC: 92858 AN: 151950 Hom.: 29285 Cov.: 31 AF XY: 0.617 AC XY: 45820 AN XY: 74290

Gnomad4 AFR AF: 0.444

Gnomad4 AMR AF: 0.706

Gnomad4 ASJ AF: 0.704

Gnomad4 EAS AF: 0.684

Gnomad4 SAS AF: 0.550

Gnomad4 FIN AF: 0.753

Gnomad4 NFE AF: 0.663

Gnomad4 OTH AF: 0.619

Alfa AF: 0.613 Hom.: 4308

Bravo AF: 0.602

Asia WGS AF: 0.629 AC: 2187 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.86
Dann	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4275453; hg19: chr1-159708047;