12-2788698-C-G

Position:

• chr12-2788698-C-G

Variant summary

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

The NR_146317.1(ITFG2-AS1):​n.433+8179G>C 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 0.322 in 152,058 control chromosomes in the GnomAD database, including 10,545 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 0.32 (10545 hom., cov: 32)
• Consequence: ITFG2-AS1 NR_146317.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITFG2-AS1	NR_146317.1	n.433+8179G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000540428.1	n.300-1211G>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48885 AN: 151940 Hom.: 10528 Cov.: 32

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.322 AC: 48950 AN: 152058 Hom.: 10545 Cov.: 32 AF XY: 0.326 AC XY: 24201 AN XY: 74310

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.483

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.313

Alfa AF: 0.116 Hom.: 191

Bravo AF: 0.338

Asia WGS AF: 0.448 AC: 1557 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.82
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2968909; hg19: chr12-2897864;