Genetic Variant KLHL7-DT:n.151-246T>A (chr7-23104563-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000419813.2(KLHL7-DT):n.151-246T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 150,870 control chromosomes in the GnomAD database, including 11,262 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 0.37 ( 11262 hom., cov: 31)

Consequence

KLHL7-DT
ENST00000419813.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0330

Publications

8 publications found

Variant links:

Genes affected

KLHL7-DT (HGNC:43431): (KLHL7 divergent transcript)

KLHL7-DT 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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KLHL7-DT	NR_046220.1 link	n.146-246T>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
KLHL7-DT	ENST00000419813.2 link	n.151-246T>A	intron_variant	Intron 1 of 2	2
KLHL7-DT	ENST00000662806.1 link	n.146-246T>A	intron_variant	Intron 1 of 2
KLHL7-DT	ENST00000753833.1 link	n.92-246T>A	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.372

AC:

56024

AN:

150752

Hom.:

11249

Cov.:

show subpopulations

Gnomad AFR

AF:

0.449

Gnomad AMI

AF:

0.301

Gnomad AMR

AF:

0.313

Gnomad ASJ

AF:

0.387

Gnomad EAS

AF:

0.169

Gnomad SAS

AF:

0.245

Gnomad FIN

AF:

0.299

Gnomad MID

AF:

0.386

Gnomad NFE

AF:

0.374

Gnomad OTH

AF:

0.399

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

GnomAD4 genome

AF:

0.372

AC:

56054

AN:

150870

Hom.:

11262

Cov.:

AF XY:

0.364

AC XY:

26809

AN XY:

73678

show subpopulations

African (AFR)

AF:

0.449

AC:

18127

AN:

40382

American (AMR)

AF:

0.312

AC:

4753

AN:

15232

Ashkenazi Jewish (ASJ)

AF:

0.387

AC:

1343

AN:

3466

East Asian (EAS)

AF:

0.169

AC:

875

AN:

5182

South Asian (SAS)

AF:

0.244

AC:

1176

AN:

4818

European-Finnish (FIN)

AF:

0.299

AC:

3158

AN:

10548

Middle Eastern (MID)

AF:

0.391

AC:

115

AN:

294

European-Non Finnish (NFE)

AF:

0.374

AC:

25386

AN:

67934

Other (OTH)

AF:

0.403

AC:

848

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1706

3412

5119

6825

8531

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

532

1064

1596

2128

2660

<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:

0.378

Hom.:

1407

Bravo

AF:

0.374

Asia WGS

AF:

0.283

AC:

985

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.8

(source)

DANN

Benign

0.56

PhyloP100

-0.033

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