rs12590640

Positions:

• chr14-36384931-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000634305.1(ENSG00000283098):​n.250+44791C>T variant causes a intron, non coding transcript 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: ENST00000634305.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.527

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000634305.1	n.250+44791C>T		intron_variant, non_coding_transcript_variant		5
	ENST00000667682.1	n.221-12228C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.664

Gnomad4 AMR AF: 0.609

Gnomad4 ASJ AF: 0.514

Gnomad4 EAS AF: 0.860

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.458

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.539

Alfa AF: 0.475 Hom.: 13719

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12590640; hg19: chr14-36854136;