rs2039528

chr1-43494859-A-G

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 0.366 in 152,110 control chromosomes in the GnomAD database, including 10,521 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 0.37 (10521 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.78

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55644 AN: 151992 Hom.: 10523 Cov.: 33

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.366 AC: 55663 AN: 152110 Hom.: 10521 Cov.: 33 AF XY: 0.370 AC XY: 27501 AN XY: 74374

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.331

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.604

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.348

Alfa AF: 0.361 Hom.: 1353

Bravo AF: 0.359

Asia WGS AF: 0.476 AC: 1655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	7.7
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2039528; hg19: chr1-43960530;