2-47179400-C-T

Variant names:

• chr2-47179400-C-T
• rs1723482
• ENST00000782148.1:n.86+3864C>T

Variant summary

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

The ENST00000782148.1(ENSG00000226087):​n.86+3864C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.776 in 152,190 control chromosomes in the GnomAD database, including 46,849 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 0.78 (46849 hom., cov: 33)
• Consequence: ENSG00000226087 ENST00000782148.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.150
• Publications: 7 publications found

Genes affected

ENSG00000226087 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.885 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
ENSG00000226087	ENST00000782148.1	n.86+3864C>T		intron_variant	Intron 1 of 3
ENSG00000226087	ENST00000782149.1	n.328+3864C>T		intron_variant	Intron 1 of 3
ENSG00000226087	ENST00000782150.1	n.322+3864C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.776 AC: 118063 AN: 152072 Hom.: 46826 Cov.: 33

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.844

Gnomad ASJ AF: 0.889

Gnomad EAS AF: 0.876

Gnomad SAS AF: 0.906

Gnomad FIN AF: 0.826

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.806

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

GnomAD4 genome AF: 0.776 AC: 118124 AN: 152190 Hom.: 46849 Cov.: 33 AF XY: 0.780 AC XY: 58040 AN XY: 74406

African (AFR) AF: 0.596 AC: 24725 AN: 41490

American (AMR) AF: 0.844 AC: 12915 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.889 AC: 3088 AN: 3472

East Asian (EAS) AF: 0.876 AC: 4545 AN: 5188

South Asian (SAS) AF: 0.908 AC: 4380 AN: 4826

European-Finnish (FIN) AF: 0.826 AC: 8758 AN: 10604

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.838 AC: 57003 AN: 68004

Other (OTH) AF: 0.807 AC: 1699 AN: 2106

Alfa AF: 0.819 Hom.: 61277

Bravo AF: 0.768

Asia WGS AF: 0.875 AC: 3040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.7
DANN	Benign	0.57
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs1723482; hg19: chr2-47406539;