12-121195980-C-T

Variant names:

• chr12-121195980-C-T
• rs2686365
• ENST00000733273.1:n.339+7518G>A

Variant summary

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

The ENST00000733273.1(ENSG00000295862):​n.339+7518G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.017 in 151,896 control chromosomes in the GnomAD database, including 65 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 0.017 (65 hom., cov: 31)
• Consequence: ENSG00000295862 ENST00000733273.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97
• Publications: 1 publications found

Genes affected

ENSG00000295862 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.056 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370032	XR_001749352.3	n.327+7518G>A		intron_variant	Intron 2 of 3
LOC105370032	XR_001749353.3	n.268+7518G>A		intron_variant	Intron 2 of 2
LOC105370032	XR_945459.4	n.304+7518G>A		intron_variant	Intron 2 of 2
LOC105370032	XR_945460.4	n.298+7518G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295862	ENST00000733273.1	n.339+7518G>A		intron_variant	Intron 2 of 2
ENSG00000295862	ENST00000733274.1	n.541+7518G>A		intron_variant	Intron 3 of 3
ENSG00000295862	ENST00000733275.1	n.257+7518G>A		intron_variant	Intron 2 of 2
ENSG00000295862	ENST00000733276.1	n.240+7518G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0170 AC: 2578 AN: 151786 Hom.: 65 Cov.: 31

Gnomad AFR AF: 0.0580

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00808

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000397

Gnomad OTH AF: 0.0153

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

GnomAD4 genome AF: 0.0170 AC: 2582 AN: 151896 Hom.: 65 Cov.: 31 AF XY: 0.0161 AC XY: 1198 AN XY: 74240

African (AFR) AF: 0.0579 AC: 2399 AN: 41430

American (AMR) AF: 0.00807 AC: 123 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5168

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4826

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10472

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.000397 AC: 27 AN: 67976

Other (OTH) AF: 0.0152 AC: 32 AN: 2112

Alfa AF: 0.00409 Hom.: 2

Bravo AF: 0.0198

Asia WGS AF: 0.00231 AC: 8 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.59
DANN	Benign	0.77
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs2686365; hg19: chr12-121633783; COSMIC: COSV69493522;