rs2147105

Variant names:

• chr14-53939347-C-T
• rs2147105
• ENST00000729148.1:n.187+4097G>A

Variant summary

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

The ENST00000729148.1(ENSG00000295303):​n.187+4097G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.458 in 152,042 control chromosomes in the GnomAD database, including 17,064 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 0.46 (17064 hom., cov: 33)
• Consequence: ENSG00000295303 ENST00000729148.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237
• Publications: 9 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.551 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+4097G>A		intron_variant	Intron 1 of 4
ENSG00000295303	ENST00000729149.1	n.140+4097G>A		intron_variant	Intron 1 of 3
ENSG00000295303	ENST00000729150.1	n.137+4097G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.458 AC: 69576 AN: 151922 Hom.: 17066 Cov.: 33

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.458 AC: 69594 AN: 152042 Hom.: 17064 Cov.: 33 AF XY: 0.458 AC XY: 34022 AN XY: 74312

African (AFR) AF: 0.275 AC: 11389 AN: 41468

American (AMR) AF: 0.489 AC: 7477 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1848 AN: 3470

East Asian (EAS) AF: 0.390 AC: 2018 AN: 5168

South Asian (SAS) AF: 0.495 AC: 2391 AN: 4830

European-Finnish (FIN) AF: 0.484 AC: 5107 AN: 10554

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.556 AC: 37766 AN: 67960

Other (OTH) AF: 0.473 AC: 998 AN: 2112

Alfa AF: 0.535 Hom.: 17978

Bravo AF: 0.449

Asia WGS AF: 0.445 AC: 1546 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.7
DANN	Benign	0.64
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs2147105; hg19: chr14-54406065;