chr1-155153542-C-T

Variant names:

• chr1-155153542-C-T
• rs4971052

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 0.424 in 151,956 control chromosomes in the GnomAD database, including 14,338 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 0.42 (14338 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.8 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: 0.424 AC: 64335 AN: 151838 Hom.: 14336 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.821

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.424 AC: 64362 AN: 151956 Hom.: 14338 Cov.: 32 AF XY: 0.430 AC XY: 31931 AN XY: 74238

Gnomad4 AFR AF: 0.357

Gnomad4 AMR AF: 0.527

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.820

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.404

Gnomad4 OTH AF: 0.409

Alfa AF: 0.254 Hom.: 603

Bravo AF: 0.431

Asia WGS AF: 0.591 AC: 2055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	12
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4971052; hg19: chr1-155126018;