Genetic Variant ENST00000593577.3:n.252+9825C>T (chr18-41584521-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 ENST00000593577.3(KC6):n.252+9825C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 152,026 control chromosomes in the GnomAD database, including 4,368 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 0.21 ( 4368 hom., cov: 32)

Consequence

KC6
ENST00000593577.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0240

Publications

5 publications found

Variant links:

Genes affected

KC6 (HGNC:):

KC6 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=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
KC6	ENST00000593577.3 link	n.252+9825C>T	intron_variant	Intron 2 of 6	4
KC6	ENST00000595135.5 link	n.309+9825C>T	intron_variant	Intron 2 of 4	3
KC6	ENST00000599934.1 link	n.126-19623C>T	intron_variant	Intron 1 of 3	4

Frequencies

GnomAD3 genomes

AF:

0.214

AC:

32505

AN:

151906

Hom.:

4366

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0541

Gnomad AMI

AF:

0.276

Gnomad AMR

AF:

0.222

Gnomad ASJ

AF:

0.258

Gnomad EAS

AF:

0.0919

Gnomad SAS

AF:

0.128

Gnomad FIN

AF:

0.406

Gnomad MID

AF:

0.197

Gnomad NFE

AF:

0.292

Gnomad OTH

AF:

0.220

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.214

AC:

32505

AN:

152026

Hom.:

4368

Cov.:

AF XY:

0.216

AC XY:

16057

AN XY:

74312

show subpopulations

African (AFR)

AF:

0.0539

AC:

2238

AN:

41484

American (AMR)

AF:

0.222

AC:

3381

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.258

AC:

894

AN:

3470

East Asian (EAS)

AF:

0.0923

AC:

477

AN:

5168

South Asian (SAS)

AF:

0.129

AC:

620

AN:

4804

European-Finnish (FIN)

AF:

0.406

AC:

4290

AN:

10566

Middle Eastern (MID)

AF:

0.204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.292

AC:

19835

AN:

67954

Other (OTH)

AF:

0.217

AC:

459

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1204

2408

3611

4815

6019

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

336

672

1008

1344

1680

<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:

0.260

Hom.:

3173

Bravo

AF:

0.192

Asia WGS

AF:

0.105

AC:

367

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.7

(source)

DANN

Benign

0.52

PhyloP100

0.024

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over