1-11922487-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 16 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: Benign. The variant received -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 rank	MANE	Protein	UniProt
KIAA2013	NM_138346.3	c.1887+149A>G		intron_variant	Intron 2 of 2	ENST00000376572.8	NP_612355.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA2013	ENST00000376572.8	c.1887+149A>G		intron_variant	Intron 2 of 2	1	NM_138346.3	ENSP00000365756.3
KIAA2013	ENST00000376576.3	c.*32A>G		3_prime_UTR_variant	Exon 2 of 2	2		ENSP00000365760.3
ENSG00000285646	ENST00000833918.1	n.236-1981T>C		intron_variant	Intron 1 of 1

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

GnomAD2 exomes AF: 0.773 AC: 94875 AN: 122710 AF XY: 0.782

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 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

African (AFR) AF: 0.918 AC: 27899 AN: 30396

American (AMR) AF: 0.614 AC: 18718 AN: 30466

Ashkenazi Jewish (ASJ) AF: 0.695 AC: 15681 AN: 22558

East Asian (EAS) AF: 0.702 AC: 24746 AN: 35266

South Asian (SAS) AF: 0.903 AC: 66951 AN: 74166

European-Finnish (FIN) AF: 0.834 AC: 39477 AN: 47324

Middle Eastern (MID) AF: 0.801 AC: 4384 AN: 5472

European-Non Finnish (NFE) AF: 0.775 AC: 819386 AN: 1057774

Other (OTH) AF: 0.792 AC: 44516 AN: 56190

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

African (AFR) AF: 0.918 AC: 38073 AN: 41484

American (AMR) AF: 0.644 AC: 9837 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.691 AC: 2398 AN: 3472

East Asian (EAS) AF: 0.761 AC: 3933 AN: 5166

South Asian (SAS) AF: 0.901 AC: 4341 AN: 4820

European-Finnish (FIN) AF: 0.828 AC: 8758 AN: 10574

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.773 AC: 52571 AN: 67972

Other (OTH) AF: 0.790 AC: 1667 AN: 2110

Alfa AF: 0.775 Hom.: 73196

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
PhyloP100		-0.38
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2639453; hg19: chr1-11982544;