rs1281317

Variant names:

• chr1-181996319-G-A
• rs1281317
• ENST00000671017.1:n.287+2380C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-181996319-G-A
• chr1-181996319-G-C

Variant summary

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

The ENST00000671017.1(ENSG00000287452):​n.287+2380C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.849 in 152,252 control chromosomes in the GnomAD database, including 55,293 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 0.85 (55293 hom., cov: 32)
• Consequence: ENSG00000287452 ENST00000671017.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114
• Publications: 3 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=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.939 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	ENST00000671017.1	n.287+2380C>T		intron_variant	Intron 1 of 1
ENSG00000287452	ENST00000717053.1	n.287+2380C>T		intron_variant	Intron 1 of 3
ENSG00000287452	ENST00000717054.1	n.292+2380C>T		intron_variant	Intron 1 of 3
ENSG00000287452	ENST00000717056.1	n.291+2380C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.849 AC: 129208 AN: 152134 Hom.: 55239 Cov.: 32

Gnomad AFR AF: 0.947

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.879

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.840

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

GnomAD4 genome AF: 0.849 AC: 129321 AN: 152252 Hom.: 55293 Cov.: 32 AF XY: 0.852 AC XY: 63381 AN XY: 74424

African (AFR) AF: 0.947 AC: 39372 AN: 41564

American (AMR) AF: 0.879 AC: 13442 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.822 AC: 2851 AN: 3470

East Asian (EAS) AF: 0.867 AC: 4495 AN: 5182

South Asian (SAS) AF: 0.853 AC: 4107 AN: 4814

European-Finnish (FIN) AF: 0.821 AC: 8686 AN: 10586

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.788 AC: 53618 AN: 68024

Other (OTH) AF: 0.841 AC: 1776 AN: 2112

Alfa AF: 0.804 Hom.: 77516

Bravo AF: 0.859

Asia WGS AF: 0.838 AC: 2913 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	5.4
DANN	Benign	0.70
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs1281317; hg19: chr1-181965454;