rs1039443

Variant names:

• chr5-16037993-T-C
• rs1039443

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 0.182 in 152,152 control chromosomes in the GnomAD database, including 3,518 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 0.18 (3518 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.843

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.357 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: 0.182 AC: 27663 AN: 152034 Hom.: 3515 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.0510

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.182 AC: 27697 AN: 152152 Hom.: 3518 Cov.: 32 AF XY: 0.178 AC XY: 13251 AN XY: 74404

Gnomad4 AFR AF: 0.361

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.0510

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.168

Alfa AF: 0.132 Hom.: 2363

Bravo AF: 0.193

Asia WGS AF: 0.179 AC: 621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.047
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1039443; hg19: chr5-16038102;