ENST00000579097.1:n.310+15123G>A

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371956	XR_935087.3	n.271+567G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000263745	ENST00000579097.1	n.310+15123G>A		intron_variant	Intron 3 of 3	2
ENSG00000263745	ENST00000582086.2	n.93+567G>A		intron_variant	Intron 1 of 3	2
ENSG00000263745	ENST00000584867.1	n.196+128716G>A		intron_variant	Intron 2 of 5	2

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 v4.3

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

Other links and lift over

dbSNP: rs476941; hg19: chr18-2111078;