NM_138346.3:c.1887+149A>C

Variant names:

• chr1-11922487-T-G
• rs2639453
• NM_138346.3:c.1887+149A>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_138346.3(KIAA2013):​c.1887+149A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000588 in 1,359,858 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 31)
  • Exomes 𝑓: 0.0000059 (0 hom.)
• Consequence: KIAA2013 NM_138346.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.382
• Publications: 0 publications found

Genes affected

KIAA2013 (HGNC:28513): (KIAA2013) Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000285646 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138346.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA2013	NM_138346.3	MANE Select	c.1887+149A>C		intron	N/A	NP_612355.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA2013	ENST00000376572.8	TSL:1 MANE Select	c.1887+149A>C		intron	N/A	ENSP00000365756.3
	KIAA2013	ENST00000376576.3	TSL:2	c.*32A>C		3_prime_UTR	Exon 2 of 2	ENSP00000365760.3
	ENSG00000285646	ENST00000833918.1		n.236-1981T>G		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 0.00000588 AC: 8 AN: 1359858 Hom.: 0 Cov.: 54 AF XY: 0.00000750 AC XY: 5 AN XY: 666436

African (AFR) AF: 0.00 AC: 0 AN: 30400

American (AMR) AF: 0.00 AC: 0 AN: 30520

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 22574

East Asian (EAS) AF: 0.00 AC: 0 AN: 35268

South Asian (SAS) AF: 0.00 AC: 0 AN: 74186

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 47326

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5476

European-Non Finnish (NFE) AF: 0.00000756 AC: 8 AN: 1057900

Other (OTH) AF: 0.00 AC: 0 AN: 56208

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.33
PhyloP100		-0.38

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: rs2639453; hg19: chr1-11982544;