dbSNP rs2703175: KC6:n.665+31997T>C (chr18-41469123-A-G) – 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.665+31997T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.888 in 152,242 control chromosomes in the GnomAD database, including 60,083 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 0.89 ( 60083 hom., cov: 32)

Consequence

KC6
ENST00000593577.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.454

Publications

1 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=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.911 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.665+31997T>C	intron_variant	Intron 5 of 6	4
KC6	ENST00000600644.3 link	n.935-1343T>C	intron_variant	Intron 4 of 4	3
ENSG00000286328	ENST00000670702.1 link	n.200-35011A>G	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.888

AC:

135040

AN:

152124

Hom.:

60036

Cov.:

show subpopulations

Gnomad AFR

AF:

0.919

Gnomad AMI

AF:

0.925

Gnomad AMR

AF:

0.844

Gnomad ASJ

AF:

0.877

Gnomad EAS

AF:

0.827

Gnomad SAS

AF:

0.801

Gnomad FIN

AF:

0.880

Gnomad MID

AF:

0.921

Gnomad NFE

AF:

0.890

Gnomad OTH

AF:

0.894

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

GnomAD4 genome

AF:

0.888

AC:

135147

AN:

152242

Hom.:

60083

Cov.:

AF XY:

0.884

AC XY:

65817

AN XY:

74424

show subpopulations

African (AFR)

AF:

0.919

AC:

38183

AN:

41544

American (AMR)

AF:

0.844

AC:

12908

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.877

AC:

3044

AN:

3472

East Asian (EAS)

AF:

0.827

AC:

4270

AN:

5166

South Asian (SAS)

AF:

0.801

AC:

3859

AN:

4816

European-Finnish (FIN)

AF:

0.880

AC:

9343

AN:

10616

Middle Eastern (MID)

AF:

0.918

AC:

270

AN:

294

European-Non Finnish (NFE)

AF:

0.890

AC:

60538

AN:

68018

Other (OTH)

AF:

0.895

AC:

1888

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

795

1589

2384

3178

3973

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

898

1796

2694

3592

4490

<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:

0.889

Hom.:

77803

Bravo

AF:

0.886

Asia WGS

AF:

0.847

AC:

2943

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.83

(source)

DANN

Benign

0.56

PhyloP100

-0.45

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