dbSNP rs2843012: KIF25-AS1:n.1099+7265C>T (chr6-167988248-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 ENST00000732089.1(KIF25-AS1):n.1099+7265C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 151,980 control chromosomes in the GnomAD database, including 8,053 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 0.32 ( 8053 hom., cov: 32)

Consequence

KIF25-AS1
ENST00000732089.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.44

Publications

7 publications found

Variant links:

Genes affected

KIF25-AS1 (HGNC:20953): (KIF25 antisense RNA 1)

KIF25-AS1 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=-0.95).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF25-AS1	ENST00000732089.1 link	n.1099+7265C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.317

AC:

48117

AN:

151862

Hom.:

8052

Cov.:

show subpopulations

Gnomad AFR

AF:

0.243

Gnomad AMI

AF:

0.279

Gnomad AMR

AF:

0.315

Gnomad ASJ

AF:

0.362

Gnomad EAS

AF:

0.0413

Gnomad SAS

AF:

0.202

Gnomad FIN

AF:

0.262

Gnomad MID

AF:

0.373

Gnomad NFE

AF:

0.397

Gnomad OTH

AF:

0.341

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

GnomAD4 genome

AF:

0.317

AC:

48123

AN:

151980

Hom.:

8053

Cov.:

AF XY:

0.307

AC XY:

22773

AN XY:

74288

show subpopulations

African (AFR)

AF:

0.243

AC:

10073

AN:

41466

American (AMR)

AF:

0.315

AC:

4803

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.362

AC:

1256

AN:

3472

East Asian (EAS)

AF:

0.0412

AC:

213

AN:

5168

South Asian (SAS)

AF:

0.202

AC:

969

AN:

4796

European-Finnish (FIN)

AF:

0.262

AC:

2776

AN:

10584

Middle Eastern (MID)

AF:

0.364

AC:

107

AN:

294

European-Non Finnish (NFE)

AF:

0.397

AC:

26954

AN:

67926

Other (OTH)

AF:

0.341

AC:

720

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1596

3193

4789

6386

7982

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

484

968

1452

1936

2420

<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:

0.360

Hom.:

15512

Bravo

AF:

0.317

Asia WGS

AF:

0.139

AC:

484

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.63

(source)

DANN

Benign

0.20

PhyloP100

-2.4

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