12-9311210-T-C

Position:

• chr12-9311210-T-C

Variant summary

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

The NR_024374.1(LOC642846):​n.2435T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.94 in 1,389,540 control chromosomes in the GnomAD database, including 617,689 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 0.91 (62918 hom., cov: 26)
  • Exomes 𝑓: 0.94 (554771 hom.)
• Consequence: LOC642846 NR_024374.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.58

Genes affected

DDX12B (HGNC:38668): (DEAD/H-box helicase 12B%2C pseudogene [Source:HGNC Symbol%3BAcc:HGNC:38668])

LOC642846 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC642846	NR_024374.1	n.2435T>C		non_coding_transcript_exon_variant	21/22

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DDX12B	ENST00000539757.1	n.2325T>C		non_coding_transcript_exon_variant	22/29

Frequencies

GnomAD3 genomes AF: 0.911 AC: 137337 AN: 150750 Hom.: 62874 Cov.: 26

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.991

Gnomad AMR AF: 0.937

Gnomad ASJ AF: 0.971

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.957

Gnomad FIN AF: 0.950

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.953

Gnomad OTH AF: 0.896

GnomAD4 exome AF: 0.944 AC: 1169282 AN: 1238674 Hom.: 554771 Cov.: 20 AF XY: 0.946 AC XY: 592119 AN XY: 626238

Gnomad4 AFR exome AF: 0.829

Gnomad4 AMR exome AF: 0.953

Gnomad4 ASJ exome AF: 0.964

Gnomad4 EAS exome AF: 0.744

Gnomad4 SAS exome AF: 0.962

Gnomad4 FIN exome AF: 0.950

Gnomad4 NFE exome AF: 0.954

Gnomad4 OTH exome AF: 0.934

GnomAD4 genome AF: 0.911 AC: 137432 AN: 150866 Hom.: 62918 Cov.: 26 AF XY: 0.910 AC XY: 67067 AN XY: 73666

Gnomad4 AFR AF: 0.835

Gnomad4 AMR AF: 0.937

Gnomad4 ASJ AF: 0.971

Gnomad4 EAS AF: 0.712

Gnomad4 SAS AF: 0.957

Gnomad4 FIN AF: 0.950

Gnomad4 NFE AF: 0.953

Gnomad4 OTH AF: 0.895

Alfa AF: 0.938 Hom.: 12373

Bravo AF: 0.903

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	17
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10771515; hg19: chr12-9463806; COSMIC: COSV62037025;