chr1-4255144-G-T

Variant names:

• chr1-4255144-G-T
• rs966321

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 0.43 in 151,960 control chromosomes in the GnomAD database, including 15,994 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 0.43 (15994 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 17 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65274 AN: 151842 Hom.: 15984 Cov.: 31

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.430 AC: 65310 AN: 151960 Hom.: 15994 Cov.: 31 AF XY: 0.436 AC XY: 32383 AN XY: 74254

African (AFR) AF: 0.180 AC: 7442 AN: 41442

American (AMR) AF: 0.528 AC: 8065 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1619 AN: 3468

East Asian (EAS) AF: 0.364 AC: 1877 AN: 5158

South Asian (SAS) AF: 0.602 AC: 2896 AN: 4808

European-Finnish (FIN) AF: 0.578 AC: 6101 AN: 10562

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.528 AC: 35859 AN: 67946

Other (OTH) AF: 0.425 AC: 895 AN: 2104

Alfa AF: 0.484 Hom.: 66137

Bravo AF: 0.410

Asia WGS AF: 0.516 AC: 1797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.087
DANN	Benign	0.67
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs966321; hg19: chr1-4315204;