rs7523017

chr1-35549410-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024874.5(KIAA0319L):c.142+4940C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0468 in 152,108 control chromosomes in the GnomAD database, including 232 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 0.047 (232 hom., cov: 32)
• Consequence: KIAA0319L NM_024874.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.85

Genes affected

KIAA0319L (HGNC:30071): (KIAA0319 like) Predicted to act upstream of or within several processes, including flagellated sperm motility; proacrosomal vesicle fusion; and receptor-mediated endocytosis of virus by host cell. Located in Golgi apparatus; cytoplasmic vesicle; and nucleolus. [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 (NFE) allele frequency at 95% confidence interval = 0.0661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA0319L	NM_024874.5	c.142+4940C>T		intron_variant		ENST00000325722.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA0319L	ENST00000325722.8	c.142+4940C>T		intron_variant		1	NM_024874.5	P1

Frequencies

GnomAD3 genomes AF: 0.0468 AC: 7116 AN: 151990 Hom.: 231 Cov.: 32

Gnomad AFR AF: 0.0120

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0478

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0663

Gnomad FIN AF: 0.0449

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0677

Gnomad OTH AF: 0.0546

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

GnomAD4 genome AF: 0.0468 AC: 7116 AN: 152108 Hom.: 232 Cov.: 32 AF XY: 0.0461 AC XY: 3431 AN XY: 74358

Gnomad4 AFR AF: 0.0120

Gnomad4 AMR AF: 0.0477

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0667

Gnomad4 FIN AF: 0.0449

Gnomad4 NFE AF: 0.0677

Gnomad4 OTH AF: 0.0541

Alfa AF: 0.0618 Hom.: 165

Bravo AF: 0.0458

Asia WGS AF: 0.0200 AC: 70 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	0.036
Dann	Benign	0.79

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: rs7523017; hg19: chr1-36015011;