rs1025039

Variant names:

• chr5-35901755-G-T
• rs1025039

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 0.41 in 152,106 control chromosomes in the GnomAD database, including 13,272 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 0.41 (13272 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.458 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: 0.411 AC: 62412 AN: 151988 Hom.: 13267 Cov.: 33

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.0940

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.410 AC: 62431 AN: 152106 Hom.: 13272 Cov.: 33 AF XY: 0.403 AC XY: 29938 AN XY: 74336

Gnomad4 AFR AF: 0.463

Gnomad4 AMR AF: 0.319

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.0944

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.400

Alfa AF: 0.416 Hom.: 6817

Bravo AF: 0.407

Asia WGS AF: 0.192 AC: 667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.6
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1025039; hg19: chr5-35901857;