rs1039443

Variant names:

• chr5-16037993-T-C
• rs1039443

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 0.182 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
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.361 AC: 14993 AN: 41490

American (AMR) AF: 0.111 AC: 1691 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 445 AN: 3468

East Asian (EAS) AF: 0.131 AC: 680 AN: 5176

South Asian (SAS) AF: 0.165 AC: 795 AN: 4822

European-Finnish (FIN) AF: 0.0510 AC: 541 AN: 10612

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 8027 AN: 67992

Other (OTH) AF: 0.168 AC: 354 AN: 2110

Alfa AF: 0.142 Hom.: 6742

Bravo AF: 0.193

Asia WGS AF: 0.179 AC: 621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.047
DANN	Benign	0.46
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs1039443; hg19: chr5-16038102;