rs12320939

Variant names:

• chr12-121624817-G-T
• rs12320939
• ENST00000786201.1:n.179+2087C>A

Variant summary

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

The ENST00000786201.1(ENSG00000302371):​n.179+2087C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 151,772 control chromosomes in the GnomAD database, including 19,642 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 0.49 (19642 hom., cov: 29)
• Consequence: ENSG00000302371 ENST00000786201.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.702
• Publications: 32 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 (AFR) allele frequency at 95% confidence interval = 0.683 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+2087C>A		intron_variant	Intron 1 of 2
ENSG00000302371	ENST00000786202.1	n.181+2087C>A		intron_variant	Intron 1 of 3
ENSG00000302371	ENST00000786203.1	n.179+2087C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74489 AN: 151654 Hom.: 19581 Cov.: 29

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.492 AC: 74618 AN: 151772 Hom.: 19642 Cov.: 29 AF XY: 0.489 AC XY: 36257 AN XY: 74176

African (AFR) AF: 0.689 AC: 28533 AN: 41394

American (AMR) AF: 0.444 AC: 6740 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1295 AN: 3466

East Asian (EAS) AF: 0.495 AC: 2549 AN: 5154

South Asian (SAS) AF: 0.457 AC: 2199 AN: 4814

European-Finnish (FIN) AF: 0.394 AC: 4155 AN: 10536

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.408 AC: 27732 AN: 67900

Other (OTH) AF: 0.446 AC: 943 AN: 2112

Alfa AF: 0.436 Hom.: 56596

Bravo AF: 0.503

Asia WGS AF: 0.506 AC: 1762 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	0.25
DANN	Benign	0.43
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs12320939; hg19: chr12-122062722;