2-202085128-G-C

Position:

• chr2-202085128-G-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001277372.4(KIAA2012):​c.370-5642G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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 Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIAA2012	NM_001277372.4	c.370-5642G>C		intron_variant		ENST00000498697.3	NP_001264301.2
KIAA2012	NM_001367720.2	c.370-5642G>C		intron_variant			NP_001354649.1
KIAA2012	XM_017003112.3	c.370-5642G>C		intron_variant			XP_016858601.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIAA2012	ENST00000498697.3	c.370-5642G>C		intron_variant		5	NM_001277372.4	ENSP00000419834	P1
KIAA2012-AS1	ENST00000409819.2	n.3214-9562C>G		intron_variant, non_coding_transcript_variant		2
KIAA2012	ENST00000459709.5	c.538-5642G>C		intron_variant		2		ENSP00000490419
KIAA2012	ENST00000409515.3	n.709-5642G>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.021
DANN	Benign	0.45

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;