rs1521882

chr2-202085128-G-Achr2-202085128-G-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

KIAA2012 (HGNC:51250): (KIAA2012)

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
KIAA2012	NM_001277372.4	c.370-5642G>A		intron_variant		ENST00000498697.3
KIAA2012	NM_001367720.2	c.370-5642G>A		intron_variant
KIAA2012	XM_017003112.3	c.370-5642G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA2012	ENST00000498697.3	c.370-5642G>A		intron_variant		5	NM_001277372.4	P1
KIAA2012-AS1	ENST00000409819.2	n.3214-9562C>T		intron_variant, non_coding_transcript_variant		2
KIAA2012	ENST00000459709.5	c.538-5642G>A		intron_variant		2
KIAA2012	ENST00000409515.3	n.709-5642G>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.855

Gnomad4 AMR AF: 0.828

Gnomad4 ASJ AF: 0.885

Gnomad4 EAS AF: 0.718

Gnomad4 SAS AF: 0.667

Gnomad4 FIN AF: 0.857

Gnomad4 NFE AF: 0.811

Gnomad4 OTH AF: 0.812

Alfa AF: 0.810 Hom.: 78992

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs1521882; hg19: chr2-202949851;