rs1039096

chr5-2433577-G-Achr5-2433577-G-C

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 0.347 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.514

Gnomad4 AMR AF: 0.270

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.326

Gnomad4 NFE AF: 0.258

Gnomad4 OTH AF: 0.302

Alfa AF: 0.296 Hom.: 3228

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1039096; hg19: chr5-2433691;