rs1159057

Variant names:

• chr4-65271097-C-T
• rs1159057

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 0.331 in 151,992 control chromosomes in the GnomAD database, including 9,285 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 0.33 (9285 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.742

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.433 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: 0.331 AC: 50344 AN: 151874 Hom.: 9272 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.331 AC: 50367 AN: 151992 Hom.: 9285 Cov.: 32 AF XY: 0.334 AC XY: 24812 AN XY: 74286

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.448

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.397

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.338

Alfa AF: 0.383 Hom.: 7440

Bravo AF: 0.320

Asia WGS AF: 0.424 AC: 1477 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1159057; hg19: chr4-66136815;