rs12920112

Variant names:

• chr16-86948799-G-A
• rs12920112
• ENST00000670133.1:n.189-6933G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000670133.1(ENSG00000287161):​n.189-6933G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,206 control chromosomes in the GnomAD database, including 2,330 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 0.17 (2330 hom., cov: 33)
• Consequence: ENSG00000287161 ENST00000670133.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.310

Genes affected

ENSG00000287161 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.248 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
ENSG00000287161	ENST00000670133.1	n.189-6933G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25417 AN: 152088 Hom.: 2327 Cov.: 33

Gnomad AFR AF: 0.0984

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.167 AC: 25420 AN: 152206 Hom.: 2330 Cov.: 33 AF XY: 0.168 AC XY: 12512 AN XY: 74414

Gnomad4 AFR AF: 0.0982

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.167

Alfa AF: 0.184 Hom.: 575

Bravo AF: 0.159

Asia WGS AF: 0.217 AC: 752 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.2
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12920112; hg19: chr16-86982405;