chr14-56720189-C-G

Variant names:

• chr14-56720189-C-G
• rs7153196
• ENST00000554597.5:n.369+5701G>C

Variant summary

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

The ENST00000554597.5(ENSG00000259133):​n.369+5701G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 152,068 control chromosomes in the GnomAD database, including 7,068 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 0.29 (7068 hom., cov: 32)
• Consequence: ENSG00000259133 ENST00000554597.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.837
• Publications: 2 publications found

Genes affected

ENSG00000259133 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.339 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
ENSG00000259133	ENST00000554597.5	n.369+5701G>C		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44500 AN: 151950 Hom.: 7073 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.293 AC: 44508 AN: 152068 Hom.: 7068 Cov.: 32 AF XY: 0.291 AC XY: 21600 AN XY: 74344

African (AFR) AF: 0.182 AC: 7563 AN: 41482

American (AMR) AF: 0.334 AC: 5105 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.491 AC: 1701 AN: 3466

East Asian (EAS) AF: 0.294 AC: 1519 AN: 5162

South Asian (SAS) AF: 0.197 AC: 949 AN: 4810

European-Finnish (FIN) AF: 0.295 AC: 3115 AN: 10564

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23328 AN: 67984

Other (OTH) AF: 0.349 AC: 737 AN: 2112

Alfa AF: 0.167 Hom.: 336

Bravo AF: 0.295

Asia WGS AF: 0.279 AC: 967 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.98
DANN	Benign	0.55
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs7153196; hg19: chr14-57186907;