dbSNP rs6682554: KIAA2013:c.-327A>G (chr1-11926564-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_138346.3(KIAA2013):c.-327A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 151,566 control chromosomes in the GnomAD database, including 25,941 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 0.58 ( 25925 hom., cov: 29)

Exomes 𝑓: 0.56 ( 16 hom. )

Consequence

KIAA2013
NM_138346.3 upstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.76

Variant links:

Genes affected

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

KIAA2013 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIAA2013	NM_138346.3 link	c.-327A>G		upstream_gene_variant		ENST00000376572.8	NP_612355.1	Q8IYS2-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA2013	ENST00000376572.8 link	c.-327A>G		upstream_gene_variant		1	NM_138346.3	ENSP00000365756.3		Q8IYS2-1
KIAA2013	ENST00000376576.3 link	c.-327A>G		upstream_gene_variant		2		ENSP00000365760.3		Q8IYS2-2

Frequencies

GnomAD3 genomes

AF:

0.580

AC:

87862

AN:

151362

Hom.:

25885

Cov.:

show subpopulations

Gnomad AFR

AF:

0.646

Gnomad AMI

AF:

0.309

Gnomad AMR

AF:

0.498

Gnomad ASJ

AF:

0.457

Gnomad EAS

AF:

0.647

Gnomad SAS

AF:

0.666

Gnomad FIN

AF:

0.633

Gnomad MID

AF:

0.443

Gnomad NFE

AF:

0.551

Gnomad OTH

AF:

0.571

GnomAD4 exome

AF:

0.561

AC:

AN:

Hom.:

AF XY:

0.559

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.750

Gnomad4 EAS exome

AF:

0.500

Gnomad4 FIN exome

AF:

0.833

Gnomad4 NFE exome

AF:

0.563

Gnomad4 OTH exome

AF:

0.250

GnomAD4 genome

AF:

0.581

AC:

87970

AN:

151484

Hom.:

25925

Cov.:

AF XY:

0.583

AC XY:

43109

AN XY:

73966

show subpopulations

Gnomad4 AFR

AF:

0.646

Gnomad4 AMR

AF:

0.499

Gnomad4 ASJ

AF:

0.457

Gnomad4 EAS

AF:

0.648

Gnomad4 SAS

AF:

0.665

Gnomad4 FIN

AF:

0.633

Gnomad4 NFE

AF:

0.551

Gnomad4 OTH

AF:

0.570

Alfa

AF:

0.564

Hom.:

11147

Bravo

AF:

0.569

Asia WGS

AF:

0.685

AC:

2379

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.1

DANN

Benign

0.60

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over