rs3909680

Variant names:

• chr12-115164442-C-T
• rs3909680
• ENST00000759060.1:n.157-6147C>T

Variant summary

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

The ENST00000759060.1(ENSG00000298928):​n.157-6147C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 151,520 control chromosomes in the GnomAD database, including 14,544 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 0.43 (14544 hom., cov: 32)
• Consequence: ENSG00000298928 ENST00000759060.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.404
• Publications: 1 publications found

Genes affected

ENSG00000298928 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903081	XR_007063589.1	n.83-6147C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298928	ENST00000759060.1	n.157-6147C>T		intron_variant	Intron 1 of 1
ENSG00000298928	ENST00000759062.1	n.321+3760C>T		intron_variant	Intron 2 of 2
ENSG00000298928	ENST00000759063.1	n.333+3760C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.429 AC: 64891 AN: 151404 Hom.: 14534 Cov.: 32

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.428 AC: 64916 AN: 151520 Hom.: 14544 Cov.: 32 AF XY: 0.429 AC XY: 31775 AN XY: 74034

African (AFR) AF: 0.329 AC: 13597 AN: 41342

American (AMR) AF: 0.575 AC: 8738 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.511 AC: 1771 AN: 3464

East Asian (EAS) AF: 0.610 AC: 3122 AN: 5116

South Asian (SAS) AF: 0.602 AC: 2891 AN: 4806

European-Finnish (FIN) AF: 0.322 AC: 3382 AN: 10500

Middle Eastern (MID) AF: 0.465 AC: 134 AN: 288

European-Non Finnish (NFE) AF: 0.442 AC: 29951 AN: 67804

Other (OTH) AF: 0.455 AC: 959 AN: 2106

Alfa AF: 0.442 Hom.: 33360

Bravo AF: 0.447

Asia WGS AF: 0.585 AC: 2034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.64
DANN	Benign	0.27
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs3909680; hg19: chr12-115602247;