3-102834680-G-T

Variant names:

• chr3-102834680-G-T
• rs1694189
• ENST00000840969.1:n.342+12316C>A

Variant summary

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

The ENST00000840969.1(ENSG00000309424):​n.342+12316C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.831 in 152,188 control chromosomes in the GnomAD database, including 52,507 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 0.83 (52507 hom., cov: 33)
• Consequence: ENSG00000309424 ENST00000840969.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.926
• Publications: 3 publications found

Genes affected

ENSG00000309424 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.872 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
ENSG00000309424	ENST00000840969.1	n.342+12316C>A		intron_variant	Intron 2 of 3
ENSG00000309424	ENST00000840970.1	n.328+12316C>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.830 AC: 126285 AN: 152070 Hom.: 52457 Cov.: 33

Gnomad AFR AF: 0.852

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.890

Gnomad SAS AF: 0.894

Gnomad FIN AF: 0.841

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.800

Gnomad OTH AF: 0.832

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

GnomAD4 genome AF: 0.831 AC: 126395 AN: 152188 Hom.: 52507 Cov.: 33 AF XY: 0.834 AC XY: 62044 AN XY: 74400

African (AFR) AF: 0.852 AC: 35380 AN: 41528

American (AMR) AF: 0.868 AC: 13265 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.783 AC: 2720 AN: 3472

East Asian (EAS) AF: 0.890 AC: 4615 AN: 5186

South Asian (SAS) AF: 0.894 AC: 4310 AN: 4822

European-Finnish (FIN) AF: 0.841 AC: 8901 AN: 10586

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.800 AC: 54424 AN: 67990

Other (OTH) AF: 0.833 AC: 1762 AN: 2116

Alfa AF: 0.775 Hom.: 2360

Bravo AF: 0.830

Asia WGS AF: 0.874 AC: 3036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.85
DANN	Benign	0.33
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs1694189; hg19: chr3-102553524;