ENST00000548963.1:n.245+15520G>A

Variant names:

• chr12-78438806-G-A
• rs2163314
• ENST00000548963.1:n.245+15520G>A

Variant summary

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

The ENST00000548963.1(ENSG00000258084):​n.245+15520G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.737 in 151,898 control chromosomes in the GnomAD database, including 41,579 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 0.74 (41579 hom., cov: 30)
• Consequence: ENSG00000258084 ENST00000548963.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 2 publications found

Genes affected

ENSG00000258084 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.911 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
ENSG00000258084	ENST00000548963.1	n.245+15520G>A		intron_variant	Intron 2 of 5	5
ENSG00000258084	ENST00000552230.5	n.163-38587G>A		intron_variant	Intron 1 of 2	3
ENSG00000258084	ENST00000654030.1	n.210-26151G>A		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.737 AC: 111820 AN: 151780 Hom.: 41533 Cov.: 30

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.933

Gnomad SAS AF: 0.869

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.716

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

GnomAD4 genome AF: 0.737 AC: 111921 AN: 151898 Hom.: 41579 Cov.: 30 AF XY: 0.740 AC XY: 54920 AN XY: 74208

African (AFR) AF: 0.799 AC: 33109 AN: 41434

American (AMR) AF: 0.746 AC: 11390 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.647 AC: 2243 AN: 3466

East Asian (EAS) AF: 0.933 AC: 4780 AN: 5122

South Asian (SAS) AF: 0.869 AC: 4182 AN: 4810

European-Finnish (FIN) AF: 0.664 AC: 6998 AN: 10542

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.688 AC: 46770 AN: 67946

Other (OTH) AF: 0.712 AC: 1497 AN: 2102

Alfa AF: 0.699 Hom.: 64069

Bravo AF: 0.742

Asia WGS AF: 0.877 AC: 3051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.33
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs2163314; hg19: chr12-78832586;