rs478801

Variant names:

• chr1-110783770-C-T
• rs478801
• ENST00000839441.1:n.*46C>T

Variant summary

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

The ENST00000839441.1(ENSG00000309193):​n.*46C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.848 in 152,224 control chromosomes in the GnomAD database, including 54,856 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 (54856 hom., cov: 32)
• Consequence: ENSG00000309193 ENST00000839441.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.822
• Publications: 4 publications found

Genes affected

ENSG00000309193 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.969 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000839441.1. 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
	ENSG00000309193	ENST00000839441.1		n.*46C>T		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.847 AC: 128906 AN: 152106 Hom.: 54795 Cov.: 32

Gnomad AFR AF: 0.871

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.882

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.991

Gnomad SAS AF: 0.887

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.817

Gnomad OTH AF: 0.854

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

GnomAD4 genome AF: 0.848 AC: 129027 AN: 152224 Hom.: 54856 Cov.: 32 AF XY: 0.851 AC XY: 63318 AN XY: 74430

African (AFR) AF: 0.872 AC: 36212 AN: 41534

American (AMR) AF: 0.882 AC: 13495 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.843 AC: 2928 AN: 3472

East Asian (EAS) AF: 0.991 AC: 5137 AN: 5182

South Asian (SAS) AF: 0.887 AC: 4282 AN: 4828

European-Finnish (FIN) AF: 0.812 AC: 8590 AN: 10584

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.817 AC: 55564 AN: 68006

Other (OTH) AF: 0.856 AC: 1811 AN: 2116

Alfa AF: 0.833 Hom.: 6839

Bravo AF: 0.857

Asia WGS AF: 0.940 AC: 3269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.54
PhyloP100		-0.82

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs478801;

hg19: chr1-111326392;