rs4650716

chr1-175159575-C-Achr1-175159575-C-Gchr1-175159575-C-T

Variant summary

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

The NM_014656.3(KIAA0040):c.*1139G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 152,230 control chromosomes in the GnomAD database, including 24,855 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 0.57 (24844 hom., cov: 33)
  • Exomes 𝑓: 0.49 (11 hom.)
• Consequence: KIAA0040 NM_014656.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740

Genes affected

KIAA0040 (HGNC:28950): (KIAA0040) Predicted to be integral component of membrane. [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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA0040	NM_014656.3	c.*1139G>T		3_prime_UTR_variant	4/4	ENST00000423313.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA0040	ENST00000423313.6	c.*1139G>T		3_prime_UTR_variant	4/4	1	NM_014656.3	P1
KIAA0040	ENST00000444639.5	c.*1139G>T		3_prime_UTR_variant	4/4	1		P1
KIAA0040	ENST00000545251.6	c.*1139G>T		3_prime_UTR_variant	3/3	1		P1
KIAA0040	ENST00000619513.1	c.*594G>T		3_prime_UTR_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.566 AC: 86022 AN: 152030 Hom.: 24808 Cov.: 33

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.863

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.579

GnomAD4 exome AF: 0.488 AC: 40 AN: 82 Hom.: 11 Cov.: 0 AF XY: 0.554 AC XY: 31 AN XY: 56

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.470

Gnomad4 NFE exome AF: 0.417

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.566 AC: 86118 AN: 152148 Hom.: 24844 Cov.: 33 AF XY: 0.571 AC XY: 42504 AN XY: 74378

Gnomad4 AFR AF: 0.590

Gnomad4 AMR AF: 0.629

Gnomad4 ASJ AF: 0.690

Gnomad4 EAS AF: 0.863

Gnomad4 SAS AF: 0.712

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.506

Gnomad4 OTH AF: 0.579

Alfa AF: 0.539 Hom.: 5420

Bravo AF: 0.580

Asia WGS AF: 0.747 AC: 2599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	1.7
Dann	Benign	0.54

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: rs4650716; hg19: chr1-175128711;