1-4384479-G-T

Variant names:

• chr1-4384479-G-T
• rs239339

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 0.182 in 151,910 control chromosomes in the GnomAD database, including 2,737 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 0.18 (2737 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.222 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: 0.182 AC: 27696 AN: 151792 Hom.: 2738 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.0747

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.182 AC: 27704 AN: 151910 Hom.: 2737 Cov.: 32 AF XY: 0.180 AC XY: 13332 AN XY: 74238

African (AFR) AF: 0.137 AC: 5687 AN: 41422

American (AMR) AF: 0.150 AC: 2289 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 905 AN: 3472

East Asian (EAS) AF: 0.0745 AC: 384 AN: 5156

South Asian (SAS) AF: 0.183 AC: 882 AN: 4810

European-Finnish (FIN) AF: 0.163 AC: 1717 AN: 10544

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15260 AN: 67926

Other (OTH) AF: 0.176 AC: 372 AN: 2108

Alfa AF: 0.204 Hom.: 7940

Bravo AF: 0.176

Asia WGS AF: 0.160 AC: 555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.44
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs239339; hg19: chr1-4444539; COSMIC: COSV59918969;