rs9804922

Positions:

• chr12-103519664-C-T

Variant summary

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

The ENST00000650784.1(ENSG00000286197):​n.205-443G>A 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 0.0982 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: ENST00000650784.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.493

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
C12orf42	XM_011538294.3	c.36+4448G>A		intron_variant
C12orf42	XM_011538306.2	c.36+4448G>A		intron_variant
C12orf42	XM_011538312.3	c.36+4448G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000650784.1	n.205-443G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.0686

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.261

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.0495

Gnomad4 NFE AF: 0.0709

Gnomad4 OTH AF: 0.105

Alfa AF: 0.0820 Hom.: 820

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

Splicing

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

Publications

LitVar

Other links and lift over

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