3-146684384-G-A

Variant names:

• chr3-146684384-G-A
• rs1912785
• ENST00000732446.1:n.82+138C>T

Variant summary

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

The ENST00000732446.1(ENSG00000295756):​n.82+138C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.551 in 151,650 control chromosomes in the GnomAD database, including 22,946 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 0.55 (22946 hom., cov: 32)
• Consequence: ENSG00000295756 ENST00000732446.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.468
• Publications: 5 publications found

Genes affected

ENSG00000295756 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000732446.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295756	ENST00000732446.1		n.82+138C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83471 AN: 151534 Hom.: 22930 Cov.: 32

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.551 AC: 83522 AN: 151650 Hom.: 22946 Cov.: 32 AF XY: 0.547 AC XY: 40514 AN XY: 74112

African (AFR) AF: 0.567 AC: 23417 AN: 41318

American (AMR) AF: 0.516 AC: 7875 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1923 AN: 3462

East Asian (EAS) AF: 0.474 AC: 2440 AN: 5144

South Asian (SAS) AF: 0.522 AC: 2511 AN: 4810

European-Finnish (FIN) AF: 0.513 AC: 5387 AN: 10504

Middle Eastern (MID) AF: 0.452 AC: 132 AN: 292

European-Non Finnish (NFE) AF: 0.563 AC: 38189 AN: 67860

Other (OTH) AF: 0.537 AC: 1132 AN: 2108

Alfa AF: 0.558 Hom.: 43487

Bravo AF: 0.551

Asia WGS AF: 0.531 AC: 1847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.9
DANN	Benign	0.78
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs1912785; hg19: chr3-146402171;