rs13375273

Variant names:

• chr1-181849948-G-A
• rs13375273
• ENST00000717053.1:n.288-14312C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-181849948-G-A
• chr1-181849948-G-T

Variant summary

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

The ENST00000717053.1(ENSG00000287452):​n.288-14312C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 152,000 control chromosomes in the GnomAD database, including 6,536 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 (6536 hom., cov: 32)
• Consequence: ENSG00000287452 ENST00000717053.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.363
• Publications: 1 publications found

Genes affected

ENSG00000287452 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.379 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
ENSG00000287452	ENST00000717053.1	n.288-14312C>T		intron_variant	Intron 1 of 3
ENSG00000287452	ENST00000717054.1	n.293-14312C>T		intron_variant	Intron 1 of 3
ENSG00000287452	ENST00000717055.1	n.81-14312C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43722 AN: 151882 Hom.: 6523 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.288 AC: 43771 AN: 152000 Hom.: 6536 Cov.: 32 AF XY: 0.289 AC XY: 21481 AN XY: 74252

African (AFR) AF: 0.212 AC: 8799 AN: 41464

American (AMR) AF: 0.294 AC: 4491 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1404 AN: 3470

East Asian (EAS) AF: 0.394 AC: 2027 AN: 5150

South Asian (SAS) AF: 0.272 AC: 1307 AN: 4812

European-Finnish (FIN) AF: 0.279 AC: 2948 AN: 10552

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21848 AN: 67954

Other (OTH) AF: 0.286 AC: 605 AN: 2114

Alfa AF: 0.288 Hom.: 999

Bravo AF: 0.285

Asia WGS AF: 0.318 AC: 1107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	6.6
DANN	Benign	0.85
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs13375273; hg19: chr1-181819083;