ENST00000548280.1:n.392+12131A>G

Variant names:

• chr14-28330663-A-G
• rs7157863
• ENST00000548280.1:n.392+12131A>G

Variant summary

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

The ENST00000548280.1(ENSG00000257869):​n.392+12131A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,288 control chromosomes in the GnomAD database, including 919 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 0.11 (919 hom., cov: 32)
• Consequence: ENSG00000257869 ENST00000548280.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.456
• Publications: 5 publications found

Genes affected

ENSG00000257869 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.123 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
ENSG00000257869	ENST00000548280.1	n.392+12131A>G		intron_variant	Intron 1 of 2	4
ENSG00000257869	ENST00000745978.1	n.309+12131A>G		intron_variant	Intron 2 of 3
ENSG00000257869	ENST00000745979.1	n.138+12480A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16590 AN: 152170 Hom.: 919 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.0727

Gnomad ASJ AF: 0.0700

Gnomad EAS AF: 0.0225

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0844

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.0946

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

GnomAD4 genome AF: 0.109 AC: 16594 AN: 152288 Hom.: 919 Cov.: 32 AF XY: 0.106 AC XY: 7889 AN XY: 74452

African (AFR) AF: 0.116 AC: 4815 AN: 41562

American (AMR) AF: 0.0725 AC: 1109 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0700 AC: 243 AN: 3470

East Asian (EAS) AF: 0.0226 AC: 117 AN: 5180

South Asian (SAS) AF: 0.119 AC: 572 AN: 4826

European-Finnish (FIN) AF: 0.0844 AC: 896 AN: 10612

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8545 AN: 68014

Other (OTH) AF: 0.0937 AC: 198 AN: 2114

Alfa AF: 0.116 Hom.: 659

Bravo AF: 0.108

Asia WGS AF: 0.0870 AC: 304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.9
DANN	Benign	0.67
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs7157863; hg19: chr14-28799869;