1-118483467-C-T

Variant names:

• chr1-118483467-C-T
• rs1146313
• ENST00000746228.1:n.579+11718G>A

Variant summary

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

The ENST00000746228.1(ENSG00000297215):​n.579+11718G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.604 in 151,956 control chromosomes in the GnomAD database, including 29,616 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 0.60 (29616 hom., cov: 32)
• Consequence: ENSG00000297215 ENST00000746228.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.519
• Publications: 1 publications found

Genes affected

ENSG00000297215 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.816 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
ENSG00000297215	ENST00000746228.1	n.579+11718G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.604 AC: 91686 AN: 151838 Hom.: 29543 Cov.: 32

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.604 AC: 91822 AN: 151956 Hom.: 29616 Cov.: 32 AF XY: 0.608 AC XY: 45187 AN XY: 74268

African (AFR) AF: 0.824 AC: 34172 AN: 41486

American (AMR) AF: 0.620 AC: 9454 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1294 AN: 3470

East Asian (EAS) AF: 0.826 AC: 4251 AN: 5146

South Asian (SAS) AF: 0.539 AC: 2595 AN: 4818

European-Finnish (FIN) AF: 0.577 AC: 6079 AN: 10542

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.476 AC: 32364 AN: 67948

Other (OTH) AF: 0.556 AC: 1171 AN: 2106

Alfa AF: 0.503 Hom.: 32075

Bravo AF: 0.621

Asia WGS AF: 0.682 AC: 2371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.62
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs1146313; hg19: chr1-119026090;