Genetic Variant KIAA0040:c.*3206C>T (chr1-175157508-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014656.3(KIAA0040):c.*3206C>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 0.874 in 152,244 control chromosomes in the GnomAD database, including 58,641 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 0.87 ( 58641 hom., cov: 32)

Failed GnomAD Quality Control

Consequence

KIAA0040
NM_014656.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.146

Publications

10 publications found

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014656.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
KIAA0040	NM_014656.3	MANE Select	c.*3206C>T	3_prime_UTR	Exon 4 of 4	NP_055471.2	Q15053
KIAA0040	NM_001162893.2		c.*3206C>T	3_prime_UTR	Exon 5 of 5	NP_001156365.1	Q15053
KIAA0040	NM_001162894.2		c.*3206C>T	3_prime_UTR	Exon 4 of 4	NP_001156366.1	Q15053

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
KIAA0040	ENST00000423313.6	TSL:1 MANE Select	c.*3206C>T	3_prime_UTR	Exon 4 of 4	ENSP00000462172.1	Q15053
KIAA0040	ENST00000444639.5	TSL:1	c.*3206C>T	3_prime_UTR	Exon 4 of 4	ENSP00000463734.1	Q15053
KIAA0040	ENST00000619513.1	TSL:2	c.*2661C>T	3_prime_UTR	Exon 2 of 2	ENSP00000478803.1	A0A384DVV8

Frequencies

GnomAD3 genomes

AF:

0.874

AC:

133009

AN:

152126

Hom.:

58573

Cov.:

show subpopulations

Gnomad AFR

AF:

0.969

Gnomad AMI

AF:

0.882

Gnomad AMR

AF:

0.894

Gnomad ASJ

AF:

0.834

Gnomad EAS

AF:

0.696

Gnomad SAS

AF:

0.725

Gnomad FIN

AF:

0.876

Gnomad MID

AF:

0.832

Gnomad NFE

AF:

0.838

Gnomad OTH

AF:

0.863

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AC:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.874

AC:

133134

AN:

152244

Hom.:

58641

Cov.:

AF XY:

0.874

AC XY:

65052

AN XY:

74432

show subpopulations

African (AFR)

AF:

0.969

AC:

40283

AN:

41554

American (AMR)

AF:

0.894

AC:

13689

AN:

15310

Ashkenazi Jewish (ASJ)

AF:

0.834

AC:

2895

AN:

3472

East Asian (EAS)

AF:

0.697

AC:

3601

AN:

5170

South Asian (SAS)

AF:

0.725

AC:

3488

AN:

4812

European-Finnish (FIN)

AF:

0.876

AC:

9281

AN:

10590

Middle Eastern (MID)

AF:

0.827

AC:

243

AN:

294

European-Non Finnish (NFE)

AF:

0.838

AC:

57026

AN:

68018

Other (OTH)

AF:

0.864

AC:

1824

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

843

1687

2530

3374

4217

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

890

1780

2670

3560

4450

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.857

Hom.:

78387

Bravo

AF:

0.881

Asia WGS

AF:

0.742

AC:

2580

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.5

(source)

DANN

Benign

0.64

PhyloP100

0.15

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over