rs116909374

Variant names:

• chr14-36269155-C-T
• rs116909374
• ENST00000729235.1:n.907G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000729235.1(ENSG00000295321):​n.907G>A 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 0.023 in 152,260 control chromosomes in the GnomAD database, including 67 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 0.023 (67 hom., cov: 32)
• Consequence: ENSG00000295321 ENST00000729235.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.749
• Publications: 61 publications found

Genes affected

ENSG00000295321 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.023 (3495/152260) while in subpopulation NFE AF = 0.0348 (2370/68026). AF 95% confidence interval is 0.0337. There are 67 homozygotes in GnomAd4. There are 1689 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 67 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000729235.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295321	ENST00000729235.1		n.907G>A		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000295321	ENST00000729236.1		n.402G>A		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0230 AC: 3496 AN: 152142 Hom.: 67 Cov.: 32

Gnomad AFR AF: 0.00719

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0184

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00476

Gnomad FIN AF: 0.0293

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0349

Gnomad OTH AF: 0.0344

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

GnomAD4 genome AF: 0.0230 AC: 3495 AN: 152260 Hom.: 67 Cov.: 32 AF XY: 0.0227 AC XY: 1689 AN XY: 74438

African (AFR) AF: 0.00717 AC: 298 AN: 41540

American (AMR) AF: 0.0184 AC: 281 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0239 AC: 83 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5176

South Asian (SAS) AF: 0.00477 AC: 23 AN: 4824

European-Finnish (FIN) AF: 0.0293 AC: 311 AN: 10598

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0348 AC: 2370 AN: 68026

Other (OTH) AF: 0.0340 AC: 72 AN: 2116

Alfa AF: 0.0289 Hom.: 172

Bravo AF: 0.0227

Asia WGS AF: 0.00520 AC: 19 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	15
DANN	Benign	0.83
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs116909374; hg19: chr14-36738361; COSMIC: COSV52393761;