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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370032	XR_001749352.3	n.327+13843T>C		intron_variant	Intron 2 of 3
LOC105370032	XR_001749353.3	n.268+13843T>C		intron_variant	Intron 2 of 2
LOC105370032	XR_945459.4	n.304+13843T>C		intron_variant	Intron 2 of 2
LOC105370032	XR_945460.4	n.298+13843T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286248	ENST00000652651.1	n.1077+746T>C		intron_variant	Intron 1 of 2
ENSG00000295862	ENST00000733273.1	n.339+13843T>C		intron_variant	Intron 2 of 2
ENSG00000295862	ENST00000733274.1	n.541+13843T>C		intron_variant	Intron 3 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs1718161; hg19: chr12-121627458;