rs1521882

Variant names:

• chr2-202085128-G-A
• rs1521882
• NM_001277372.4:c.370-5642G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-202085128-G-A
• chr2-202085128-G-C

Variant summary

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

The NM_001277372.4(KIAA2012):​c.370-5642G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.821 in 152,194 control chromosomes in the GnomAD database, including 51,531 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 0.82 (51531 hom., cov: 33)
• Consequence: KIAA2012 NM_001277372.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.682
• Publications: 13 publications found

Genes affected

KIAA2012 (HGNC:51250): (KIAA2012)

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIAA2012	NM_001277372.4	c.370-5642G>A		intron_variant	Intron 2 of 23	ENST00000498697.3	NP_001264301.2
KIAA2012	NM_001367720.2	c.370-5642G>A		intron_variant	Intron 2 of 23		NP_001354649.1
KIAA2012	XM_017003112.3	c.370-5642G>A		intron_variant	Intron 2 of 12		XP_016858601.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA2012	ENST00000498697.3	c.370-5642G>A		intron_variant	Intron 2 of 23	5	NM_001277372.4	ENSP00000419834.2

Frequencies

GnomAD3 genomes AF: 0.821 AC: 124841 AN: 152076 Hom.: 51474 Cov.: 33

Gnomad AFR AF: 0.855

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.828

Gnomad ASJ AF: 0.885

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.857

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.811

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.821 AC: 124960 AN: 152194 Hom.: 51531 Cov.: 33 AF XY: 0.822 AC XY: 61157 AN XY: 74406

African (AFR) AF: 0.855 AC: 35538 AN: 41546

American (AMR) AF: 0.828 AC: 12659 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.885 AC: 3070 AN: 3470

East Asian (EAS) AF: 0.718 AC: 3704 AN: 5162

South Asian (SAS) AF: 0.667 AC: 3219 AN: 4826

European-Finnish (FIN) AF: 0.857 AC: 9065 AN: 10580

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.811 AC: 55182 AN: 68012

Other (OTH) AF: 0.812 AC: 1715 AN: 2112

Alfa AF: 0.813 Hom.: 170246

Bravo AF: 0.819

Asia WGS AF: 0.676 AC: 2353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.025
DANN	Benign	0.47
PhyloP100		-0.68
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1521882; hg19: chr2-202949851;