rs8045387

Variant names:

• chr16-85047242-C-T
• rs8045387
• NM_001388359.1:c.-173+19384C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001388359.1(KIAA0513):​c.-173+19384C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 152,096 control chromosomes in the GnomAD database, including 13,631 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 0.40 (13631 hom., cov: 33)
• Consequence: KIAA0513 NM_001388359.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330
• Publications: 9 publications found

Genes affected

KIAA0513 (HGNC:29058): (KIAA0513) Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000299192 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001388359.1. 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
	KIAA0513	NM_001388359.1	MANE Select	c.-173+19384C>T		intron	N/A	NP_001375288.1	O60268-1
	KIAA0513	NM_014732.4		c.-173+19391C>T		intron	N/A	NP_055547.1	O60268-1
	KIAA0513	NM_001286566.2		c.-173+19384C>T		intron	N/A	NP_001273495.1	O60268-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA0513	ENST00000683363.1	MANE Select	c.-173+19384C>T		intron	N/A	ENSP00000507772.1	O60268-1
	KIAA0513	ENST00000567328.6	TSL:1	c.-173+19391C>T		intron	N/A	ENSP00000455544.1	O60268-2
	KIAA0513	ENST00000899391.1		c.-173+19391C>T		intron	N/A	ENSP00000569450.1

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60901 AN: 151978 Hom.: 13608 Cov.: 33

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.401 AC: 60969 AN: 152096 Hom.: 13631 Cov.: 33 AF XY: 0.398 AC XY: 29568 AN XY: 74326

African (AFR) AF: 0.605 AC: 25136 AN: 41522

American (AMR) AF: 0.337 AC: 5153 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1304 AN: 3466

East Asian (EAS) AF: 0.201 AC: 1036 AN: 5164

South Asian (SAS) AF: 0.407 AC: 1962 AN: 4822

European-Finnish (FIN) AF: 0.268 AC: 2832 AN: 10562

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.325 AC: 22065 AN: 67976

Other (OTH) AF: 0.392 AC: 827 AN: 2108

Alfa AF: 0.346 Hom.: 37086

Bravo AF: 0.412

Asia WGS AF: 0.305 AC: 1061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	3.0
DANN	Benign	0.65
PhyloP100		0.33
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: rs8045387; hg19: chr16-85080848;