rs12590640

Variant names:

• chr14-36384931-C-T
• rs12590640
• ENST00000634305.1:n.250+44791C>T

Variant summary

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

The ENST00000634305.1(ENSG00000283098):​n.250+44791C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 152,090 control chromosomes in the GnomAD database, including 23,184 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 0.54 (23184 hom., cov: 33)
• Consequence: ENSG00000283098 ENST00000634305.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.527
• Publications: 3 publications found

Genes affected

ENSG00000283098 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.839 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
ENSG00000283098	ENST00000634305.1	n.250+44791C>T		intron_variant	Intron 2 of 3	5
ENSG00000283098	ENST00000667682.1	n.221-12228C>T		intron_variant	Intron 2 of 3
ENSG00000283098	ENST00000716758.1	n.404-2517C>T		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81877 AN: 151972 Hom.: 23150 Cov.: 33

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.539 AC: 81961 AN: 152090 Hom.: 23184 Cov.: 33 AF XY: 0.544 AC XY: 40423 AN XY: 74338

African (AFR) AF: 0.664 AC: 27568 AN: 41504

American (AMR) AF: 0.609 AC: 9298 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1782 AN: 3470

East Asian (EAS) AF: 0.860 AC: 4454 AN: 5180

South Asian (SAS) AF: 0.558 AC: 2690 AN: 4820

European-Finnish (FIN) AF: 0.458 AC: 4835 AN: 10564

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29599 AN: 67976

Other (OTH) AF: 0.539 AC: 1141 AN: 2116

Alfa AF: 0.481 Hom.: 41511

Bravo AF: 0.557

Asia WGS AF: 0.731 AC: 2540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.3
DANN	Benign	0.49
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs12590640; hg19: chr14-36854136;