chr12-121189655-A-G

Variant names:

• chr12-121189655-A-G
• rs1718161
• ENST00000652651.1:n.1077+746T>C

Variant summary

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

The ENST00000652651.1(ENSG00000286248):​n.1077+746T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 151,914 control chromosomes in the GnomAD database, including 3,280 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 0.20 (3280 hom., cov: 31)
• Consequence: ENSG00000286248 ENST00000652651.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.370
• Publications: 6 publications found

Genes affected

ENSG00000286248 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652651.1. 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
	ENSG00000286248	ENST00000652651.1		n.1077+746T>C		intron	N/A
	ENSG00000295862	ENST00000733273.1		n.339+13843T>C		intron	N/A
	ENSG00000295862	ENST00000733274.1		n.541+13843T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30149 AN: 151796 Hom.: 3278 Cov.: 31

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.0647

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.199 AC: 30163 AN: 151914 Hom.: 3280 Cov.: 31 AF XY: 0.194 AC XY: 14371 AN XY: 74248

African (AFR) AF: 0.276 AC: 11406 AN: 41376

American (AMR) AF: 0.130 AC: 1987 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 474 AN: 3466

East Asian (EAS) AF: 0.0643 AC: 332 AN: 5162

South Asian (SAS) AF: 0.107 AC: 514 AN: 4806

European-Finnish (FIN) AF: 0.223 AC: 2349 AN: 10554

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12483 AN: 67952

Other (OTH) AF: 0.191 AC: 403 AN: 2106

Alfa AF: 0.178 Hom.: 4401

Bravo AF: 0.194

Asia WGS AF: 0.121 AC: 420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	3.2
DANN	Benign	0.86
PhyloP100		0.37

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1718161;

hg19: chr12-121627458;