rs7153196

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr14-56720189-C-G
• chr14-56720189-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000259133 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.491

Gnomad4 EAS AF: 0.294

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.349

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7153196; hg19: chr14-57186907;