14-75494193-A-G

Variant names:

• chr14-75494193-A-G
• rs7155603
• ENST00000751543.1:n.159-3400T>C

Variant summary

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

The ENST00000751543.1(ENSG00000297883):​n.159-3400T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 152,016 control chromosomes in the GnomAD database, including 4,695 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 0.24 (4695 hom., cov: 31)
• Consequence: ENSG00000297883 ENST00000751543.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.571
• Publications: 20 publications found

Genes affected

ENSG00000297883 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751543.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297883	ENST00000751543.1		n.159-3400T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36975 AN: 151898 Hom.: 4677 Cov.: 31

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.244 AC: 37046 AN: 152016 Hom.: 4695 Cov.: 31 AF XY: 0.251 AC XY: 18682 AN XY: 74292

African (AFR) AF: 0.273 AC: 11319 AN: 41450

American (AMR) AF: 0.287 AC: 4392 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 370 AN: 3470

East Asian (EAS) AF: 0.296 AC: 1528 AN: 5158

South Asian (SAS) AF: 0.205 AC: 990 AN: 4818

European-Finnish (FIN) AF: 0.334 AC: 3518 AN: 10546

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14339 AN: 67980

Other (OTH) AF: 0.212 AC: 448 AN: 2110

Alfa AF: 0.216 Hom.: 6235

Bravo AF: 0.243

Asia WGS AF: 0.264 AC: 918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.8
DANN	Benign	0.82
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs7155603; hg19: chr14-75960536;