rs1514673

Variant names:

• chr12-43250350-C-T
• rs1514673
• ENST00000793185.1:n.63-4138C>T

Variant summary

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

The ENST00000793185.1(ENSG00000303249):​n.63-4138C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 152,050 control chromosomes in the GnomAD database, including 5,364 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 0.26 (5364 hom., cov: 31)
• Consequence: ENSG00000303249 ENST00000793185.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.653
• Publications: 1 publications found

Genes affected

ENSG00000303249 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.506 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
ENSG00000303249	ENST00000793185.1	n.63-4138C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39580 AN: 151932 Hom.: 5365 Cov.: 31

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.260 AC: 39592 AN: 152050 Hom.: 5364 Cov.: 31 AF XY: 0.261 AC XY: 19373 AN XY: 74324

African (AFR) AF: 0.273 AC: 11334 AN: 41478

American (AMR) AF: 0.266 AC: 4069 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1024 AN: 3468

East Asian (EAS) AF: 0.522 AC: 2695 AN: 5158

South Asian (SAS) AF: 0.197 AC: 952 AN: 4822

European-Finnish (FIN) AF: 0.235 AC: 2479 AN: 10568

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16201 AN: 67964

Other (OTH) AF: 0.273 AC: 576 AN: 2112

Alfa AF: 0.246 Hom.: 805

Bravo AF: 0.264

Asia WGS AF: 0.371 AC: 1291 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.22
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs1514673; hg19: chr12-43644153;