rs476941

Variant names:

• chr18-2111077-C-T
• rs476941
• ENST00000579097.1:n.310+15123G>A

Variant summary

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

The ENST00000579097.1(ENSG00000263745):​n.310+15123G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.697 in 151,982 control chromosomes in the GnomAD database, including 36,942 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 0.70 (36942 hom., cov: 31)
• Consequence: ENSG00000263745 ENST00000579097.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 3 publications found

Genes affected

ENSG00000263745 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000579097.1. 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
	ENSG00000263745	ENST00000579097.1	TSL:2	n.310+15123G>A		intron	N/A
	ENSG00000263745	ENST00000582086.2	TSL:2	n.93+567G>A		intron	N/A
	ENSG00000263745	ENST00000584867.1	TSL:2	n.196+128716G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.697 AC: 105902 AN: 151864 Hom.: 36921 Cov.: 31

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.754

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.697 AC: 105980 AN: 151982 Hom.: 36942 Cov.: 31 AF XY: 0.698 AC XY: 51890 AN XY: 74314

African (AFR) AF: 0.714 AC: 29546 AN: 41404

American (AMR) AF: 0.651 AC: 9936 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.731 AC: 2537 AN: 3470

East Asian (EAS) AF: 0.665 AC: 3444 AN: 5180

South Asian (SAS) AF: 0.713 AC: 3426 AN: 4802

European-Finnish (FIN) AF: 0.754 AC: 7980 AN: 10580

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.691 AC: 46945 AN: 67966

Other (OTH) AF: 0.679 AC: 1431 AN: 2106

Alfa AF: 0.689 Hom.: 39895

Bravo AF: 0.688

Asia WGS AF: 0.687 AC: 2390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.29
DANN	Benign	0.36
PhyloP100		-1.2

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: rs476941;

hg19: chr18-2111078;