chr1-35557258-C-T

Position:

• chr1-35557258-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_024874.5(KIAA0319L):​c.-80G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0394 in 208,670 control chromosomes in the GnomAD database, including 464 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 0.049 (435 hom., cov: 33)
  • Exomes 𝑓: 0.013 (29 hom.)
• Consequence: KIAA0319L NM_024874.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.50

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIAA0319L	NM_024874.5	c.-80G>A		5_prime_UTR_variant	1/21	ENST00000325722.8	NP_079150.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIAA0319L	ENST00000325722.8	c.-80G>A		5_prime_UTR_variant	1/21	1	NM_024874.5	ENSP00000318406.3

Frequencies

GnomAD3 genomes AF: 0.0493 AC: 7506 AN: 152180 Hom.: 434 Cov.: 33

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0770

Gnomad ASJ AF: 0.00202

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.0284

Gnomad FIN AF: 0.0241

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00287

Gnomad OTH AF: 0.0458

GnomAD4 exome AF: 0.0126 AC: 711 AN: 56372 Hom.: 29 Cov.: 0 AF XY: 0.0126 AC XY: 392 AN XY: 31114

Gnomad4 AFR exome AF: 0.0528

Gnomad4 AMR exome AF: 0.0652

Gnomad4 ASJ exome AF: 0.00198

Gnomad4 EAS exome AF: 0.169

Gnomad4 SAS exome AF: 0.0137

Gnomad4 FIN exome AF: 0.0204

Gnomad4 NFE exome AF: 0.00322

Gnomad4 OTH exome AF: 0.0146

GnomAD4 genome AF: 0.0494 AC: 7519 AN: 152298 Hom.: 435 Cov.: 33 AF XY: 0.0516 AC XY: 3839 AN XY: 74464

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.0774

Gnomad4 ASJ AF: 0.00202

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.0282

Gnomad4 FIN AF: 0.0241

Gnomad4 NFE AF: 0.00287

Gnomad4 OTH AF: 0.0458

Alfa AF: 0.00338 Hom.: 0

Bravo AF: 0.0585

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	19
DANN	Benign	0.93

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: rs28366021; hg19: chr1-36022859;