16-85047242-C-T

Position:

• chr16-85047242-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIAA0513	NM_001388359.1	c.-173+19384C>T		intron_variant		ENST00000683363.1	NP_001375288.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIAA0513	ENST00000683363.1	c.-173+19384C>T		intron_variant			NM_001388359.1	ENSP00000507772	A1
KIAA0513	ENST00000567328.6	c.-173+19391C>T		intron_variant		1		ENSP00000455544
KIAA0513	ENST00000538274.6	c.-173+19384C>T		intron_variant		2		ENSP00000446439	P4

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

Gnomad4 AFR AF: 0.605

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.376

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.392

Alfa AF: 0.337 Hom.: 15141

Bravo AF: 0.412

Asia WGS AF: 0.305 AC: 1061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	3.0
DANN	Benign	0.65

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: rs8045387; hg19: chr16-85080848;