1-4255144-G-T

Variant names:

• chr1-4255144-G-T
• rs966321

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 0.43 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.430 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

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.364

Gnomad4 SAS AF: 0.602

Gnomad4 FIN AF: 0.578

Gnomad4 NFE AF: 0.528

Gnomad4 OTH AF: 0.425

Alfa AF: 0.496 Hom.: 28173

Bravo AF: 0.410

Asia WGS AF: 0.516 AC: 1797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs966321; hg19: chr1-4315204;