Variant rs4650716 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0740

Variant links:

Genes affected

KIAA0040 (HGNC:28950): (KIAA0040) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

KIAA0040 links:

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ACMG classification

Classification made for transcript

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	Protein	UniProt
KIAA0040	NM_014656.3 linkuse as main transcript	c.*1139G>T		3_prime_UTR_variant	4/4	ENST00000423313.6	NP_055471.2

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris
KIAA0040	ENST00000423313.6 linkuse as main transcript	c.*1139G>T	3_prime_UTR_variant	4/4	1	NM_014656.3	ENSP00000462172	P1
KIAA0040	ENST00000444639.5 linkuse as main transcript	c.*1139G>T	3_prime_UTR_variant	4/4	1		ENSP00000463734	P1
KIAA0040	ENST00000545251.6 linkuse as main transcript	c.*1139G>T	3_prime_UTR_variant	3/3	1		ENSP00000464040	P1
KIAA0040	ENST00000619513.1 linkuse as main transcript	c.*594G>T	3_prime_UTR_variant	2/2	2		ENSP00000478803

Frequencies

GnomAD3 genomes

AF:

0.566

AC:

86022

AN:

152030

Hom.:

24808

Cov.:

show subpopulations

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:

AN:

Hom.:

Cov.:

AF XY:

0.554

AC XY:

AN XY:

show subpopulations

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.:

AF XY:

0.571

AC XY:

42504

AN XY:

74378

show subpopulations

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over