rs3742555

Variant names:

• chr14-53918751-A-T
• rs3742555
• ENST00000729148.1:n.188-1839T>A

Variant summary

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

The ENST00000729148.1(ENSG00000295303):​n.188-1839T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,026 control chromosomes in the GnomAD database, including 998 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 0.11 (998 hom., cov: 32)
• Consequence: ENSG00000295303 ENST00000729148.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.18 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.188-1839T>A		intron_variant	Intron 1 of 4
ENSG00000295303	ENST00000729149.1	n.141-1839T>A		intron_variant	Intron 1 of 3
ENSG00000295303	ENST00000729150.1	n.138-1839T>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16285 AN: 151910 Hom.: 991 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0905

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0728

Gnomad OTH AF: 0.0872

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

GnomAD4 genome AF: 0.107 AC: 16326 AN: 152026 Hom.: 998 Cov.: 32 AF XY: 0.111 AC XY: 8250 AN XY: 74308

African (AFR) AF: 0.157 AC: 6480 AN: 41392

American (AMR) AF: 0.110 AC: 1680 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0905 AC: 314 AN: 3468

East Asian (EAS) AF: 0.103 AC: 532 AN: 5166

South Asian (SAS) AF: 0.191 AC: 918 AN: 4816

European-Finnish (FIN) AF: 0.113 AC: 1200 AN: 10598

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0728 AC: 4953 AN: 67992

Other (OTH) AF: 0.0919 AC: 194 AN: 2110

Alfa AF: 0.105 Hom.: 123

Bravo AF: 0.104

Asia WGS AF: 0.171 AC: 594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.49
DANN	Benign	0.66
PhyloP100		-0.077

Splicing

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

Other links and lift over

dbSNP: rs3742555; hg19: chr14-54385469;