rs1039096

Variant names:

• chr5-2433577-G-A
• rs1039096

Your query was ambiguous. Multiple possible variants found:

• chr5-2433577-G-A
• chr5-2433577-G-C

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 0.347 in 152,030 control chromosomes in the GnomAD database, including 10,323 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 0.35 (10323 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.509 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: 0.347 AC: 52684 AN: 151912 Hom.: 10295 Cov.: 33

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.347 AC: 52755 AN: 152030 Hom.: 10323 Cov.: 33 AF XY: 0.353 AC XY: 26220 AN XY: 74312

African (AFR) AF: 0.514 AC: 21307 AN: 41426

American (AMR) AF: 0.270 AC: 4128 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1065 AN: 3470

East Asian (EAS) AF: 0.462 AC: 2387 AN: 5170

South Asian (SAS) AF: 0.418 AC: 2018 AN: 4822

European-Finnish (FIN) AF: 0.326 AC: 3443 AN: 10550

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.258 AC: 17527 AN: 67988

Other (OTH) AF: 0.302 AC: 638 AN: 2112

Alfa AF: 0.294 Hom.: 3595

Bravo AF: 0.345

Asia WGS AF: 0.443 AC: 1537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.082
DANN	Benign	0.35
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs1039096; hg19: chr5-2433691;