rs9804922

Variant names:

• chr12-103519664-C-T
• rs9804922
• ENST00000650784.1:n.205-443G>A

Variant summary

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

The ENST00000650784.1(ENSG00000286197):​n.205-443G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0982 in 152,104 control chromosomes in the GnomAD database, including 953 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 0.098 (953 hom., cov: 32)
• Consequence: ENSG00000286197 ENST00000650784.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.493
• Publications: 3 publications found

Genes affected

ENSG00000286197 (HGNC:):

C12orf42 (HGNC:24729): (chromosome 12 open reading frame 42)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C12orf42	XM_047428802.1	c.36+4448G>A		intron_variant	Intron 2 of 6		XP_047284758.1
C12orf42	XM_047428803.1	c.-21-41217G>A		intron_variant	Intron 1 of 5		XP_047284759.1
C12orf42	XM_011538294.3	c.36+4448G>A		intron_variant	Intron 2 of 5		XP_011536596.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286197	ENST00000650784.1	n.205-443G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0981 AC: 14904 AN: 151986 Hom.: 950 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0687

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.0495

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0709

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0982 AC: 14930 AN: 152104 Hom.: 953 Cov.: 32 AF XY: 0.101 AC XY: 7475 AN XY: 74344

African (AFR) AF: 0.125 AC: 5194 AN: 41480

American (AMR) AF: 0.0686 AC: 1048 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 418 AN: 3472

East Asian (EAS) AF: 0.261 AC: 1347 AN: 5170

South Asian (SAS) AF: 0.267 AC: 1286 AN: 4810

European-Finnish (FIN) AF: 0.0495 AC: 525 AN: 10612

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0709 AC: 4822 AN: 67972

Other (OTH) AF: 0.105 AC: 222 AN: 2110

Alfa AF: 0.0826 Hom.: 1035

Bravo AF: 0.0977

Asia WGS AF: 0.273 AC: 947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.5
DANN	Benign	0.47
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs9804922; hg19: chr12-103913442; COSMIC: COSV50457708;