14-20442073-G-T

Position:

• chr14-20442073-G-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000291038 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.20442073G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000291038	ENST00000687238.1	n.880G>T		non_coding_transcript_exon_variant	6/8
ENSG00000291038	ENST00000700970.1	n.658G>T		non_coding_transcript_exon_variant	4/5

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

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.455

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.380

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

Splicing

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

Publications

LitVar

Other links and lift over

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