rs12313273

Variant names:

• chr12-121625105-T-C
• rs12313273
• ENST00000786201.1:n.179+1799A>G

Variant summary

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

The ENST00000786201.1(ENSG00000302371):​n.179+1799A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 151,890 control chromosomes in the GnomAD database, including 4,283 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 0.23 (4283 hom., cov: 29)
• Consequence: ENSG00000302371 ENST00000786201.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.468
• Publications: 39 publications found

Genes affected

ENSG00000302371 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302371	ENST00000786201.1	n.179+1799A>G		intron_variant	Intron 1 of 2
ENSG00000302371	ENST00000786202.1	n.181+1799A>G		intron_variant	Intron 1 of 3
ENSG00000302371	ENST00000786203.1	n.179+1799A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34581 AN: 151772 Hom.: 4271 Cov.: 29

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.228 AC: 34639 AN: 151890 Hom.: 4283 Cov.: 29 AF XY: 0.231 AC XY: 17140 AN XY: 74272

African (AFR) AF: 0.283 AC: 11712 AN: 41384

American (AMR) AF: 0.275 AC: 4193 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 853 AN: 3468

East Asian (EAS) AF: 0.286 AC: 1476 AN: 5152

South Asian (SAS) AF: 0.366 AC: 1762 AN: 4816

European-Finnish (FIN) AF: 0.142 AC: 1501 AN: 10580

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12337 AN: 67948

Other (OTH) AF: 0.233 AC: 491 AN: 2104

Alfa AF: 0.206 Hom.: 6235

Bravo AF: 0.238

Asia WGS AF: 0.353 AC: 1228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.9
DANN	Benign	0.42
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs12313273; hg19: chr12-122063010;