rs7523017

Variant names:

• chr1-35549410-G-A
• rs7523017
• NM_024874.5:c.142+4940C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

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]

KIAA0319L Gene-Disease associations (from GenCC):

• systemic lupus erythematosus

  Inheritance: Unknown Classification: SUPPORTIVE Submitted by: Orphanet

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 (NFE) allele frequency at 95% confidence interval = 0.0661 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024874.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA0319L	NM_024874.5	MANE Select	c.142+4940C>T		intron	N/A	NP_079150.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA0319L	ENST00000325722.8	TSL:1 MANE Select	c.142+4940C>T		intron	N/A	ENSP00000318406.3
	KIAA0319L	ENST00000426982.7	TSL:5	c.142+4940C>T		intron	N/A	ENSP00000395883.3
	KIAA0319L	ENST00000469892.7	TSL:5	c.142+4940C>T		intron	N/A	ENSP00000419396.2

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

African (AFR) AF: 0.0120 AC: 496 AN: 41494

American (AMR) AF: 0.0477 AC: 728 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 349 AN: 3470

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5184

South Asian (SAS) AF: 0.0667 AC: 321 AN: 4810

European-Finnish (FIN) AF: 0.0449 AC: 476 AN: 10592

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0677 AC: 4603 AN: 67984

Other (OTH) AF: 0.0541 AC: 114 AN: 2108

Alfa AF: 0.0536 Hom.: 217

Bravo AF: 0.0458

Asia WGS AF: 0.0200 AC: 70 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	0.036
DANN	Benign	0.79
PhyloP100		-2.8
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: rs7523017; hg19: chr1-36015011;