rs2049192

Variant names:

• chr2-202144649-T-C
• rs2049192
• NM_001277372.4:c.1908+6141T>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.1908+6141T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 152,002 control chromosomes in the GnomAD database, including 7,889 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 0.32 (7889 hom., cov: 33)
• Consequence: KIAA2012 NM_001277372.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.183
• Publications: 1 publications found

Genes affected

KIAA2012 (HGNC:51250): (KIAA2012)

ENSG00000287041 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001277372.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA2012	NM_001277372.4	MANE Select	c.1908+6141T>C		intron	N/A	NP_001264301.2	H7C5G6
	KIAA2012	NM_001367720.2		c.1905+6141T>C		intron	N/A	NP_001354649.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA2012	ENST00000498697.3	TSL:5 MANE Select	c.1908+6141T>C		intron	N/A	ENSP00000419834.2	H7C5G6
	KIAA2012	ENST00000469462.1	TSL:1	n.2793+6141T>C		intron	N/A
	KIAA2012	ENST00000409515.3	TSL:2	n.2321+6141T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.316 AC: 48004 AN: 151884 Hom.: 7878 Cov.: 33

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.0862

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.316 AC: 48040 AN: 152002 Hom.: 7889 Cov.: 33 AF XY: 0.313 AC XY: 23284 AN XY: 74314

African (AFR) AF: 0.392 AC: 16242 AN: 41440

American (AMR) AF: 0.292 AC: 4459 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 780 AN: 3470

East Asian (EAS) AF: 0.0862 AC: 445 AN: 5160

South Asian (SAS) AF: 0.333 AC: 1600 AN: 4808

European-Finnish (FIN) AF: 0.343 AC: 3623 AN: 10572

Middle Eastern (MID) AF: 0.305 AC: 89 AN: 292

European-Non Finnish (NFE) AF: 0.293 AC: 19937 AN: 67966

Other (OTH) AF: 0.299 AC: 631 AN: 2108

Alfa AF: 0.299 Hom.: 3490

Bravo AF: 0.312

Asia WGS AF: 0.240 AC: 833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.6
DANN	Benign	0.52
PhyloP100		0.18
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: rs2049192; hg19: chr2-203009372;