chr16-85059142-T-C

Variant names:

• chr16-85059142-T-C
• rs8056742
• NM_001388359.1:c.-172-7758T>C

Variant summary

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

The NM_001388359.1(KIAA0513):​c.-172-7758T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,140 control chromosomes in the GnomAD database, including 5,001 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 0.21 (5001 hom., cov: 32)
• Consequence: KIAA0513 NM_001388359.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120
• Publications: 20 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIAA0513	NM_001388359.1	c.-172-7758T>C		intron_variant	Intron 1 of 12	ENST00000683363.1	NP_001375288.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA0513	ENST00000683363.1	c.-172-7758T>C		intron_variant	Intron 1 of 12		NM_001388359.1	ENSP00000507772.1
KIAA0513	ENST00000567328.6	c.-172-7758T>C		intron_variant	Intron 1 of 7	1		ENSP00000455544.1
ENSG00000299192	ENST00000761486.1	n.802T>C		non_coding_transcript_exon_variant	Exon 3 of 3
KIAA0513	ENST00000538274.6	c.-172-7758T>C		intron_variant	Intron 1 of 11	2		ENSP00000446439.1

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31452 AN: 152022 Hom.: 4984 Cov.: 32

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.0960

Gnomad EAS AF: 0.0146

Gnomad SAS AF: 0.0514

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.207 AC: 31510 AN: 152140 Hom.: 5001 Cov.: 32 AF XY: 0.201 AC XY: 14943 AN XY: 74392

African (AFR) AF: 0.448 AC: 18571 AN: 41436

American (AMR) AF: 0.117 AC: 1787 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0960 AC: 333 AN: 3470

East Asian (EAS) AF: 0.0150 AC: 78 AN: 5186

South Asian (SAS) AF: 0.0514 AC: 248 AN: 4824

European-Finnish (FIN) AF: 0.112 AC: 1184 AN: 10604

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8721 AN: 68012

Other (OTH) AF: 0.177 AC: 374 AN: 2112

Alfa AF: 0.150 Hom.: 7441

Bravo AF: 0.216

Asia WGS AF: 0.0700 AC: 243 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.3
DANN	Benign	0.52
PhyloP100		0.012
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: rs8056742; hg19: chr16-85092748;