16-85059142-T-C

Position:

• chr16-85059142-T-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

KIAA0513 (HGNC:29058): (KIAA0513) Predicted to be located in cytoplasm. [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=-0.99).
• 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/exons	MANE	UniProt
KIAA0513	NM_001388359.1	c.-172-7758T>C		intron_variant		ENST00000683363.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA0513	ENST00000683363.1	c.-172-7758T>C		intron_variant			NM_001388359.1	A1
KIAA0513	ENST00000567328.6	c.-172-7758T>C		intron_variant		1
KIAA0513	ENST00000538274.6	c.-172-7758T>C		intron_variant		2		P4

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

Gnomad4 AFR AF: 0.448

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.0960

Gnomad4 EAS AF: 0.0150

Gnomad4 SAS AF: 0.0514

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.177

Alfa AF: 0.133 Hom.: 2216

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs8056742; hg19: chr16-85092748;