rs2639453

chr1-11922487-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_138346.3(KIAA2013):c.1887+149A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.783 in 1,511,682 control chromosomes in the GnomAD database, including 466,835 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 0.81 (50022 hom., cov: 31)
  • Exomes 𝑓: 0.78 (416813 hom.)
• Consequence: KIAA2013 NM_138346.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.382

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.91 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA2013	NM_138346.3	c.1887+149A>G		intron_variant		ENST00000376572.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA2013	ENST00000376572.8	c.1887+149A>G		intron_variant		1	NM_138346.3	P1
KIAA2013	ENST00000376576.3	c.*32A>G		3_prime_UTR_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.805 AC: 122288 AN: 151950 Hom.: 49957 Cov.: 31

Gnomad AFR AF: 0.918

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.761

Gnomad SAS AF: 0.900

Gnomad FIN AF: 0.828

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.788

GnomAD3 exomes AF: 0.773 AC: 94875 AN: 122710 Hom.: 37372 AF XY: 0.782 AC XY: 51001 AN XY: 65228

Gnomad AFR exome AF: 0.920

Gnomad AMR exome AF: 0.599

Gnomad ASJ exome AF: 0.705

Gnomad EAS exome AF: 0.771

Gnomad SAS exome AF: 0.902

Gnomad FIN exome AF: 0.832

Gnomad NFE exome AF: 0.770

Gnomad OTH exome AF: 0.762

GnomAD4 exome AF: 0.781 AC: 1061758 AN: 1359612 Hom.: 416813 Cov.: 54 AF XY: 0.784 AC XY: 522370 AN XY: 666296

Gnomad4 AFR exome AF: 0.918

Gnomad4 AMR exome AF: 0.614

Gnomad4 ASJ exome AF: 0.695

Gnomad4 EAS exome AF: 0.702

Gnomad4 SAS exome AF: 0.903

Gnomad4 FIN exome AF: 0.834

Gnomad4 NFE exome AF: 0.775

Gnomad4 OTH exome AF: 0.792

GnomAD4 genome AF: 0.805 AC: 122417 AN: 152070 Hom.: 50022 Cov.: 31 AF XY: 0.804 AC XY: 59737 AN XY: 74340

Gnomad4 AFR AF: 0.918

Gnomad4 AMR AF: 0.644

Gnomad4 ASJ AF: 0.691

Gnomad4 EAS AF: 0.761

Gnomad4 SAS AF: 0.901

Gnomad4 FIN AF: 0.828

Gnomad4 NFE AF: 0.773

Gnomad4 OTH AF: 0.790

Alfa AF: 0.773 Hom.: 57903

Bravo AF: 0.791

Asia WGS AF: 0.861 AC: 2994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	2.4
Dann	Benign	0.23

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2639453; hg19: chr1-11982544;