14-20442073-G-T

Variant names:

• chr14-20442073-G-T
• rs12050102
• ENST00000687238.1:n.880G>T

Variant summary

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

The ENST00000687238.1(ENSG00000291038):​n.880G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 151,962 control chromosomes in the GnomAD database, including 9,833 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 0.36 (9833 hom., cov: 32)
• Consequence: ENSG00000291038 ENST00000687238.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.150
• Publications: 7 publications found

Genes affected

ENSG00000291038 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.453 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
ENSG00000291038	ENST00000687238.1	n.880G>T		non_coding_transcript_exon_variant	Exon 6 of 8
ENSG00000291038	ENST00000700970.2	n.658G>T		non_coding_transcript_exon_variant	Exon 4 of 5
ENSG00000291038	ENST00000800199.1	n.806G>T		non_coding_transcript_exon_variant	Exon 6 of 8

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54125 AN: 151844 Hom.: 9824 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.356 AC: 54166 AN: 151962 Hom.: 9833 Cov.: 32 AF XY: 0.360 AC XY: 26740 AN XY: 74246

African (AFR) AF: 0.353 AC: 14608 AN: 41420

American (AMR) AF: 0.269 AC: 4109 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1577 AN: 3468

East Asian (EAS) AF: 0.368 AC: 1893 AN: 5146

South Asian (SAS) AF: 0.469 AC: 2263 AN: 4824

European-Finnish (FIN) AF: 0.429 AC: 4519 AN: 10526

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23862 AN: 67990

Other (OTH) AF: 0.380 AC: 800 AN: 2108

Alfa AF: 0.215 Hom.: 481

Bravo AF: 0.341

Asia WGS AF: 0.422 AC: 1467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.6
DANN	Benign	0.84
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs12050102; hg19: chr14-20910232; COSMIC: COSV52833613;