rs12087334

Variant names:

• chr1-116344833-C-A
• rs12087334
• ENST00000813531.1:n.268-8486G>T

Variant summary

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

The ENST00000813531.1(ENSG00000287217):​n.268-8486G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 151,972 control chromosomes in the GnomAD database, including 14,170 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 0.28 (14170 hom., cov: 32)
• Consequence: ENSG00000287217 ENST00000813531.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.554
• Publications: 4 publications found

Genes affected

ENSG00000287217 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.801 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
ENSG00000287217	ENST00000813531.1	n.268-8486G>T		intron_variant	Intron 2 of 6
ENSG00000287217	ENST00000813532.1	n.268-8486G>T		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42319 AN: 151854 Hom.: 14110 Cov.: 32

Gnomad AFR AF: 0.808

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.0284

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.0289

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.0690

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.279 AC: 42429 AN: 151972 Hom.: 14170 Cov.: 32 AF XY: 0.271 AC XY: 20105 AN XY: 74286

African (AFR) AF: 0.808 AC: 33492 AN: 41438

American (AMR) AF: 0.137 AC: 2097 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 369 AN: 3468

East Asian (EAS) AF: 0.0284 AC: 147 AN: 5168

South Asian (SAS) AF: 0.133 AC: 639 AN: 4822

European-Finnish (FIN) AF: 0.0289 AC: 305 AN: 10560

Middle Eastern (MID) AF: 0.154 AC: 45 AN: 292

European-Non Finnish (NFE) AF: 0.0690 AC: 4689 AN: 67932

Other (OTH) AF: 0.213 AC: 449 AN: 2106

Alfa AF: 0.149 Hom.: 6425

Bravo AF: 0.309

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.40
DANN	Benign	0.37
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs12087334; hg19: chr1-116887455;