1-155153542-C-T

Variant names:

• chr1-155153542-C-T
• rs4971052

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.357 AC: 14804 AN: 41426

American (AMR) AF: 0.527 AC: 8042 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1267 AN: 3464

East Asian (EAS) AF: 0.820 AC: 4248 AN: 5178

South Asian (SAS) AF: 0.480 AC: 2316 AN: 4822

European-Finnish (FIN) AF: 0.463 AC: 4876 AN: 10524

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.404 AC: 27464 AN: 67974

Other (OTH) AF: 0.409 AC: 863 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	12
DANN	Benign	0.91
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs4971052; hg19: chr1-155126018;