rs17043388

Variant names:

• chr3-5719016-T-A
• rs17043388

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 0.0841 in 152,122 control chromosomes in the GnomAD database, including 895 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 0.084 (895 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.494

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.187 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: 0.0839 AC: 12755 AN: 152004 Hom.: 886 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.0576

Gnomad ASJ AF: 0.0571

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0236

Gnomad FIN AF: 0.0372

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0442

Gnomad OTH AF: 0.0823

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

GnomAD4 genome AF: 0.0841 AC: 12791 AN: 152122 Hom.: 895 Cov.: 32 AF XY: 0.0820 AC XY: 6098 AN XY: 74388

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.0575

Gnomad4 ASJ AF: 0.0571

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0234

Gnomad4 FIN AF: 0.0372

Gnomad4 NFE AF: 0.0442

Gnomad4 OTH AF: 0.0819

Alfa AF: 0.0688 Hom.: 70

Bravo AF: 0.0898

Asia WGS AF: 0.0260 AC: 90 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.15
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17043388; hg19: chr3-5760703;