12-50761880-C-T

Variant names:

• chr12-50761880-C-T
• rs11169552
• ENST00000750012.1:n.97+2372G>A

Variant summary

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

The ENST00000750012.1(ENSG00000297678):​n.97+2372G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 151,988 control chromosomes in the GnomAD database, including 4,981 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 0.24 (4981 hom., cov: 32)
• Consequence: ENSG00000297678 ENST00000750012.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145
• Publications: 99 publications found

Genes affected

ENSG00000297678 (HGNC:58960):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000750012.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297678	ENST00000750012.1		n.97+2372G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35831 AN: 151870 Hom.: 4972 Cov.: 32

Gnomad AFR AF: 0.0912

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.236 AC: 35852 AN: 151988 Hom.: 4981 Cov.: 32 AF XY: 0.246 AC XY: 18289 AN XY: 74294

African (AFR) AF: 0.0910 AC: 3775 AN: 41474

American (AMR) AF: 0.291 AC: 4442 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1053 AN: 3466

East Asian (EAS) AF: 0.401 AC: 2072 AN: 5164

South Asian (SAS) AF: 0.332 AC: 1603 AN: 4824

European-Finnish (FIN) AF: 0.366 AC: 3849 AN: 10516

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18137 AN: 67956

Other (OTH) AF: 0.228 AC: 480 AN: 2108

Alfa AF: 0.258 Hom.: 21747

Bravo AF: 0.223

Asia WGS AF: 0.332 AC: 1153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.0
DANN	Benign	0.45
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs11169552; hg19: chr12-51155663; COSMIC: COSV50393930;