12-115427498-T-C

Variant names:

• chr12-115427498-T-C
• rs10161338
• ENST00000793387.1:n.150-20167A>G

Variant summary

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

The ENST00000793387.1(ENSG00000303287):​n.150-20167A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 151,838 control chromosomes in the GnomAD database, including 11,680 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 0.31 (11680 hom., cov: 31)
• Consequence: ENSG00000303287 ENST00000793387.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170
• Publications: 8 publications found

Genes affected

ENSG00000303287 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000793387.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303287	ENST00000793387.1		n.150-20167A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47022 AN: 151718 Hom.: 11631 Cov.: 31

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.165

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.0956

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.310 AC: 47136 AN: 151838 Hom.: 11680 Cov.: 31 AF XY: 0.311 AC XY: 23047 AN XY: 74200

African (AFR) AF: 0.661 AC: 27357 AN: 41362

American (AMR) AF: 0.264 AC: 4018 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 814 AN: 3470

East Asian (EAS) AF: 0.592 AC: 3043 AN: 5142

South Asian (SAS) AF: 0.336 AC: 1618 AN: 4818

European-Finnish (FIN) AF: 0.0956 AC: 1007 AN: 10536

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8440 AN: 67966

Other (OTH) AF: 0.294 AC: 617 AN: 2102

Alfa AF: 0.200 Hom.: 12260

Bravo AF: 0.341

Asia WGS AF: 0.467 AC: 1624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.2
DANN	Benign	0.63
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs10161338; hg19: chr12-115865303;