rs239339

Positions:

• chr1-4384479-G-T

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 0.182 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.0745

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.176

Alfa AF: 0.209 Hom.: 2737

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

Splicing

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

Publications

LitVar

Other links and lift over

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