rs12578202

Positions:

• chr12-103547286-G-A
• chr12-103547286-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000650784.1(ENSG00000286197):​n.204+16361C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,104 control chromosomes in the GnomAD database, including 1,663 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 0.13 (1663 hom., cov: 32)
• Consequence: ENST00000650784.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C12orf42	XM_047428803.1	c.-22+16361C>T		intron_variant			XP_047284759.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000650784.1	n.204+16361C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20466 AN: 151986 Hom.: 1657 Cov.: 32

Gnomad AFR AF: 0.0563

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.135 AC: 20483 AN: 152104 Hom.: 1663 Cov.: 32 AF XY: 0.138 AC XY: 10267 AN XY: 74350

Gnomad4 AFR AF: 0.0563

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.272

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.157

Alfa AF: 0.157 Hom.: 1815

Bravo AF: 0.129

Asia WGS AF: 0.252 AC: 877 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.050
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12578202; hg19: chr12-103941064;