rs12457810

Variant names:

• chr18-9088652-T-G
• rs12457810
• ENST00000827765.1:n.264+5116A>C

Variant summary

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

The ENST00000827765.1(ENSG00000288939):​n.264+5116A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0721 in 152,278 control chromosomes in the GnomAD database, including 448 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 0.072 (448 hom., cov: 32)
• Consequence: ENSG00000288939 ENST00000827765.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.517
• Publications: 7 publications found

Genes affected

ENSG00000288939 (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 (EAS) allele frequency at 95% confidence interval = 0.122 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
ENSG00000288939	ENST00000827765.1	n.264+5116A>C		intron_variant	Intron 2 of 3
ENSG00000288939	ENST00000827767.1	n.241+5116A>C		intron_variant	Intron 2 of 4
ENSG00000307687	ENST00000827902.1	n.376+4587T>G		intron_variant	Intron 3 of 3
ENSG00000307687	ENST00000827903.1	n.288+4587T>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0720 AC: 10949 AN: 152160 Hom.: 443 Cov.: 32

Gnomad AFR AF: 0.0577

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0975

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0262

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0718

Gnomad OTH AF: 0.0837

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

GnomAD4 genome AF: 0.0721 AC: 10973 AN: 152278 Hom.: 448 Cov.: 32 AF XY: 0.0712 AC XY: 5304 AN XY: 74456

African (AFR) AF: 0.0578 AC: 2401 AN: 41564

American (AMR) AF: 0.0978 AC: 1496 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 481 AN: 3472

East Asian (EAS) AF: 0.130 AC: 673 AN: 5184

South Asian (SAS) AF: 0.106 AC: 512 AN: 4820

European-Finnish (FIN) AF: 0.0262 AC: 278 AN: 10620

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0718 AC: 4881 AN: 68006

Other (OTH) AF: 0.0903 AC: 191 AN: 2114

Alfa AF: 0.0745 Hom.: 1566

Bravo AF: 0.0769

Asia WGS AF: 0.151 AC: 523 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	1.5
DANN	Benign	0.77
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs12457810; hg19: chr18-9088650;