rs298158

Variant names:

• chr1-60405454-G-A
• rs298158
• ENST00000794751.1:n.393-11556C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-60405454-G-A
• chr1-60405454-G-C
• chr1-60405454-G-T

Variant summary

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

The ENST00000794751.1(ENSG00000303463):​n.393-11556C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0488 in 152,130 control chromosomes in the GnomAD database, including 472 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 0.049 (472 hom., cov: 32)
• Consequence: ENSG00000303463 ENST00000794751.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.553
• Publications: 1 publications found

Genes affected

ENSG00000303463 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.14 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
ENSG00000303463	ENST00000794751.1	n.393-11556C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0488 AC: 7412 AN: 152012 Hom.: 476 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0187

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.0472

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.000661

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00388

Gnomad OTH AF: 0.0388

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

GnomAD4 genome AF: 0.0488 AC: 7418 AN: 152130 Hom.: 472 Cov.: 32 AF XY: 0.0504 AC XY: 3749 AN XY: 74366

African (AFR) AF: 0.139 AC: 5771 AN: 41480

American (AMR) AF: 0.0187 AC: 286 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0101 AC: 35 AN: 3468

East Asian (EAS) AF: 0.0475 AC: 246 AN: 5174

South Asian (SAS) AF: 0.149 AC: 721 AN: 4824

European-Finnish (FIN) AF: 0.000661 AC: 7 AN: 10586

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.00387 AC: 263 AN: 68000

Other (OTH) AF: 0.0388 AC: 82 AN: 2112

Alfa AF: 0.000469 Hom.: 54

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.5
DANN	Benign	0.16
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs298158; hg19: chr1-60871126;