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. The variant received -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
• Publications: 5 publications found

Genes affected

ENSG00000258784 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0191 AC: 793 AN: 41562

American (AMR) AF: 0.0791 AC: 1210 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0170 AC: 59 AN: 3472

East Asian (EAS) AF: 0.454 AC: 2347 AN: 5174

South Asian (SAS) AF: 0.104 AC: 500 AN: 4828

European-Finnish (FIN) AF: 0.0184 AC: 195 AN: 10610

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.00588 AC: 400 AN: 68036

Other (OTH) AF: 0.0369 AC: 78 AN: 2112

Alfa AF: 0.0205 Hom.: 905

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
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs7494275; hg19: chr14-56231800;