rs7494275

Variant names:

• chr14-55765082-A-C
• rs7494275
• ENST00000554458.1:n.76-6549A>C

Your query was ambiguous. Multiple possible variants found:

• chr14-55765082-A-C
• chr14-55765082-A-G
• chr14-55765082-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000554458.1(ENSG00000258784):​n.76-6549A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0367 in 152,302 control chromosomes in the GnomAD database, including 658 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 0.037 (658 hom., cov: 33)
• Consequence: ENSG00000258784 ENST00000554458.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.190

Genes affected

ENSG00000258784 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.438 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
ENSG00000258784	ENST00000554458.1	n.76-6549A>C		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.0366 AC: 5573 AN: 152184 Hom.: 653 Cov.: 33

Gnomad AFR AF: 0.0191

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0783

Gnomad ASJ AF: 0.0170

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.0184

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00588

Gnomad OTH AF: 0.0349

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

GnomAD4 genome AF: 0.0367 AC: 5585 AN: 152302 Hom.: 658 Cov.: 33 AF XY: 0.0417 AC XY: 3108 AN XY: 74478

Gnomad4 AFR AF: 0.0191

Gnomad4 AMR AF: 0.0791

Gnomad4 ASJ AF: 0.0170

Gnomad4 EAS AF: 0.454

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.0184

Gnomad4 NFE AF: 0.00588

Gnomad4 OTH AF: 0.0369

Alfa AF: 0.0187 Hom.: 603

Bravo AF: 0.0439

Asia WGS AF: 0.273 AC: 951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7494275; hg19: chr14-56231800;