ENST00000729148.1:n.187+2970C>G

Variant names:

• chr14-53940474-G-C
• rs1951867
• ENST00000729148.1:n.187+2970C>G

Variant summary

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

The ENST00000729148.1(ENSG00000295303):​n.187+2970C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.06 in 152,212 control chromosomes in the GnomAD database, including 342 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 0.060 (342 hom., cov: 33)
• Consequence: ENSG00000295303 ENST00000729148.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.446
• Publications: 6 publications found

Genes affected

ENSG00000295303 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0921 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
ENSG00000295303	ENST00000729148.1	n.187+2970C>G		intron_variant	Intron 1 of 4
ENSG00000295303	ENST00000729149.1	n.140+2970C>G		intron_variant	Intron 1 of 3
ENSG00000295303	ENST00000729150.1	n.137+2970C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0600 AC: 9121 AN: 152094 Hom.: 341 Cov.: 33

Gnomad AFR AF: 0.0944

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0435

Gnomad ASJ AF: 0.0749

Gnomad EAS AF: 0.0849

Gnomad SAS AF: 0.0394

Gnomad FIN AF: 0.0358

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0451

Gnomad OTH AF: 0.0731

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

GnomAD4 genome AF: 0.0600 AC: 9137 AN: 152212 Hom.: 342 Cov.: 33 AF XY: 0.0585 AC XY: 4352 AN XY: 74412

African (AFR) AF: 0.0945 AC: 3926 AN: 41526

American (AMR) AF: 0.0434 AC: 664 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0749 AC: 260 AN: 3470

East Asian (EAS) AF: 0.0843 AC: 437 AN: 5184

South Asian (SAS) AF: 0.0395 AC: 190 AN: 4816

European-Finnish (FIN) AF: 0.0358 AC: 380 AN: 10604

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0451 AC: 3068 AN: 67996

Other (OTH) AF: 0.0742 AC: 157 AN: 2116

Alfa AF: 0.0539 Hom.: 34

Bravo AF: 0.0644

Asia WGS AF: 0.0540 AC: 186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.8
DANN	Benign	0.57
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs1951867; hg19: chr14-54407192;