Genetic Variant ENST00000625367.2:n.308A>G (chr1-44105456-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 ENST00000625367.2(ENSG00000230615):n.308A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 151,808 control chromosomes in the GnomAD database, including 6,630 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 0.29 ( 6628 hom., cov: 31)

Exomes 𝑓: 0.30 ( 2 hom. )

Consequence

ENSG00000230615
ENST00000625367.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.121

Publications

1 publications found

Variant links:

Genes affected

ENSG00000230615 (HGNC:):

ENSG00000230615 links:

KLF17 (HGNC:18830): (KLF transcription factor 17) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to act upstream of or within gamete generation. Predicted to be located in nucleus. Predicted to be part of chromatin. [provided by Alliance of Genome Resources, Apr 2022]

KLF17 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=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein
KLF17	XM_011540700.2 link	c.-30-23897A>G	intron_variant	Intron 4 of 6	XP_011539002.1
KLF17	XM_047445936.1 link	c.-30-23897A>G	intron_variant	Intron 2 of 4	XP_047301892.1
KLF17	XM_047445938.1 link	c.-30-23897A>G	intron_variant	Intron 2 of 4	XP_047301894.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000230615	ENST00000625367.2 link	n.308A>G	non_coding_transcript_exon_variant	Exon 2 of 3	5
ENSG00000230615	ENST00000627824.2 link	n.633A>G	non_coding_transcript_exon_variant	Exon 2 of 3	5
ENSG00000230615	ENST00000627999.1 link	n.224A>G	non_coding_transcript_exon_variant	Exon 2 of 4	5

Frequencies

GnomAD3 genomes

AF:

0.289

AC:

43904

AN:

151684

Hom.:

6624

Cov.:

show subpopulations

Gnomad AFR

AF:

0.196

Gnomad AMI

AF:

0.409

Gnomad AMR

AF:

0.322

Gnomad ASJ

AF:

0.382

Gnomad EAS

AF:

0.328

Gnomad SAS

AF:

0.336

Gnomad FIN

AF:

0.337

Gnomad MID

AF:

0.348

Gnomad NFE

AF:

0.318

Gnomad OTH

AF:

0.316

GnomAD4 exome

AF:

0.300

AC:

AN:

Hom.:

Cov.:

AF XY:

0.143

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.289

AC:

43929

AN:

151788

Hom.:

6628

Cov.:

AF XY:

0.292

AC XY:

21634

AN XY:

74150

show subpopulations

African (AFR)

AF:

0.196

AC:

8108

AN:

41386

American (AMR)

AF:

0.322

AC:

4905

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.382

AC:

1325

AN:

3468

East Asian (EAS)

AF:

0.329

AC:

1700

AN:

5162

South Asian (SAS)

AF:

0.337

AC:

1621

AN:

4806

European-Finnish (FIN)

AF:

0.337

AC:

3525

AN:

10472

Middle Eastern (MID)

AF:

0.330

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.318

AC:

21609

AN:

67932

Other (OTH)

AF:

0.317

AC:

668

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1582

3165

4747

6330

7912

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

464

928

1392

1856

2320

<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:

0.309

Hom.:

1486

Bravo

AF:

0.286

Asia WGS

AF:

0.327

AC:

1139

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

5.5

(source)

DANN

Benign

0.79

PhyloP100

-0.12

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over