rs12992463

Positions:

• chr2-22328233-A-C
• chr2-22328233-A-G

Variant summary

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

The ENST00000450551.1(ENSG00000228999):​n.71-117239T>G 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 0.37 in 152,102 control chromosomes in the GnomAD database, including 11,767 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 0.37 (11767 hom., cov: 32)
• Consequence: ENST00000450551.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.593

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000450551.1	n.71-117239T>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56243 AN: 151984 Hom.: 11771 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.370 AC: 56238 AN: 152102 Hom.: 11767 Cov.: 32 AF XY: 0.363 AC XY: 27010 AN XY: 74344

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.442

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.361

Alfa AF: 0.463 Hom.: 33087

Bravo AF: 0.355

Asia WGS AF: 0.244 AC: 847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.10
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12992463; hg19: chr2-22551105;