1-60405454-G-C

Variant names:

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

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>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,124 control chromosomes in the GnomAD database, including 1,110 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 0.11 (1110 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 (NFE) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000794751.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303463	ENST00000794751.1		n.393-11556C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.112 AC: 17093 AN: 152006 Hom.: 1109 Cov.: 32

Gnomad AFR AF: 0.0704

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.0970

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0458

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.112 AC: 17096 AN: 152124 Hom.: 1110 Cov.: 32 AF XY: 0.111 AC XY: 8249 AN XY: 74358

African (AFR) AF: 0.0704 AC: 2920 AN: 41494

American (AMR) AF: 0.0969 AC: 1481 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 397 AN: 3466

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5174

South Asian (SAS) AF: 0.0460 AC: 222 AN: 4822

European-Finnish (FIN) AF: 0.155 AC: 1635 AN: 10582

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 9994 AN: 67986

Other (OTH) AF: 0.104 AC: 220 AN: 2112

Alfa AF: 0.0553 Hom.: 54

Bravo AF: 0.111

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.35
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;