rs2039528

Variant names:

• chr1-43494859-A-G
• rs2039528

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 0.366 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.335 AC: 13910 AN: 41470

American (AMR) AF: 0.331 AC: 5062 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1087 AN: 3470

East Asian (EAS) AF: 0.604 AC: 3126 AN: 5178

South Asian (SAS) AF: 0.435 AC: 2099 AN: 4826

European-Finnish (FIN) AF: 0.435 AC: 4602 AN: 10590

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24691 AN: 67980

Other (OTH) AF: 0.348 AC: 736 AN: 2112

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
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs2039528; hg19: chr1-43960530;