2-202039083-G-A

Variant names:

• chr2-202039083-G-A
• rs12474408
• ENST00000733168.1:n.958C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000733168.1(KIAA2012-AS1):​n.958C>T 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 0.271 in 151,790 control chromosomes in the GnomAD database, including 5,980 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 0.27 (5980 hom., cov: 31)
• Consequence: KIAA2012-AS1 ENST00000733168.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.99
• Publications: 8 publications found

Genes affected

KIAA2012-AS1 (HGNC:41164): (KIAA2012 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA2012-AS1	ENST00000733168.1	n.958C>T		non_coding_transcript_exon_variant	Exon 3 of 3
KIAA2012-AS1	ENST00000733169.1	n.*189C>T		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41137 AN: 151672 Hom.: 5978 Cov.: 31

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.00599

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.271 AC: 41168 AN: 151790 Hom.: 5980 Cov.: 31 AF XY: 0.268 AC XY: 19893 AN XY: 74142

African (AFR) AF: 0.252 AC: 10439 AN: 41410

American (AMR) AF: 0.261 AC: 3985 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 608 AN: 3464

East Asian (EAS) AF: 0.00620 AC: 32 AN: 5160

South Asian (SAS) AF: 0.109 AC: 522 AN: 4806

European-Finnish (FIN) AF: 0.364 AC: 3814 AN: 10480

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21065 AN: 67914

Other (OTH) AF: 0.235 AC: 495 AN: 2102

Alfa AF: 0.202 Hom.: 584

Bravo AF: 0.263

Asia WGS AF: 0.0960 AC: 334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	16
DANN	Benign	0.53
PhyloP100		3.0

Splicing

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

Other links and lift over

dbSNP: rs12474408; hg19: chr2-202903806;