3-143169201-C-T

Variant names:

• chr3-143169201-C-T
• rs17572584
• ENST00000840693.1:n.83+3554G>A

Variant summary

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

The ENST00000840693.1(ENSG00000309389):​n.83+3554G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,146 control chromosomes in the GnomAD database, including 939 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 0.11 (939 hom., cov: 32)
• Consequence: ENSG00000309389 ENST00000840693.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.50
• Publications: 3 publications found

Genes affected

ENSG00000309389 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.112 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
ENSG00000309389	ENST00000840693.1	n.83+3554G>A		intron_variant	Intron 1 of 1
ENSG00000309389	ENST00000840694.1	n.64+3554G>A		intron_variant	Intron 1 of 2
ENSG00000309389	ENST00000840695.1	n.62+3554G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16304 AN: 152028 Hom.: 937 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.0729

Gnomad ASJ AF: 0.0752

Gnomad EAS AF: 0.0270

Gnomad SAS AF: 0.0592

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.0997

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

GnomAD4 genome AF: 0.107 AC: 16314 AN: 152146 Hom.: 939 Cov.: 32 AF XY: 0.106 AC XY: 7918 AN XY: 74380

African (AFR) AF: 0.115 AC: 4778 AN: 41500

American (AMR) AF: 0.0727 AC: 1113 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0752 AC: 261 AN: 3470

East Asian (EAS) AF: 0.0271 AC: 140 AN: 5174

South Asian (SAS) AF: 0.0592 AC: 285 AN: 4814

European-Finnish (FIN) AF: 0.155 AC: 1641 AN: 10592

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7743 AN: 67984

Other (OTH) AF: 0.101 AC: 213 AN: 2108

Alfa AF: 0.106 Hom.: 1569

Bravo AF: 0.101

Asia WGS AF: 0.0560 AC: 195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.080
DANN	Benign	0.46
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs17572584; hg19: chr3-142888043;