rs17043388

Variant names:

• chr3-5719016-T-A
• rs17043388
• ENST00000425894.2:n.291+22530T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000425894.2(ENSG00000229642):​n.291+22530T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000229642 ENST00000425894.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.494
• Publications: 1 publications found

Genes affected

ENSG00000229642 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000425894.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000229642	ENST00000425894.2	TSL:3	n.291+22530T>A		intron	N/A
	ENSG00000229642	ENST00000779001.1		n.212+22530T>A		intron	N/A
	ENSG00000229642	ENST00000779002.1		n.232+22530T>A		intron	N/A

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

African (AFR) AF: 0.191 AC: 7903 AN: 41474

American (AMR) AF: 0.0575 AC: 879 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0571 AC: 198 AN: 3470

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5176

South Asian (SAS) AF: 0.0234 AC: 113 AN: 4820

European-Finnish (FIN) AF: 0.0372 AC: 394 AN: 10594

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0442 AC: 3005 AN: 67996

Other (OTH) AF: 0.0819 AC: 173 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.15
DANN	Benign	0.70
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs17043388; hg19: chr3-5760703;