rs12692432

Positions:

• chr2-11115214-C-T

Variant summary

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

The NR_040080.1(FLJ33534):​n.984+5549G>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 0.436 in 152,032 control chromosomes in the GnomAD database, including 15,347 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 0.44 (15347 hom., cov: 32)
• Consequence: FLJ33534 NR_040080.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.513

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FLJ33534	NR_040080.1	n.984+5549G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000544306.5	n.793+5549G>A		intron_variant, non_coding_transcript_variant		5
	ENST00000536743.5	n.984+5549G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66303 AN: 151914 Hom.: 15337 Cov.: 32

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.436 AC: 66338 AN: 152032 Hom.: 15347 Cov.: 32 AF XY: 0.437 AC XY: 32442 AN XY: 74304

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.507

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.502

Gnomad4 NFE AF: 0.512

Gnomad4 OTH AF: 0.469

Alfa AF: 0.462 Hom.: 2087

Bravo AF: 0.426

Asia WGS AF: 0.468 AC: 1630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.1
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12692432; hg19: chr2-11255340;