dbSNP rs10485212: KCNQ5-DT:n.2250+221C>T (chr6-72617630-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NR_186827.1(KCNQ5-DT):n.304+221C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0905 in 152,230 control chromosomes in the GnomAD database, including 1,621 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 0.090 ( 1621 hom., cov: 33)

Consequence

KCNQ5-DT
NR_186827.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.839

Publications

1 publications found

Variant links:

Genes affected

KCNQ5-DT (HGNC:55469): (KCNQ5 divergent transcript)

KCNQ5-DT links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NR_186827.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.8).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_186827.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCNQ5-DT	NR_186827.1		n.304+221C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCNQ5-DT	ENST00000649228.1		n.2250+221C>T		intron	N/A
	KCNQ5-DT	ENST00000664828.1		n.2520+221C>T		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0903

AC:

13738

AN:

152112

Hom.:

1618

Cov.:

show subpopulations

Gnomad AFR

AF:

0.276

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0600

Gnomad ASJ

AF:

0.00518

Gnomad EAS

AF:

0.0213

Gnomad SAS

AF:

0.0318

Gnomad FIN

AF:

0.0151

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.0118

Gnomad OTH

AF:

0.0660

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

GnomAD4 genome

AF:

0.0905

AC:

13770

AN:

152230

Hom.:

1621

Cov.:

AF XY:

0.0884

AC XY:

6578

AN XY:

74442

show subpopulations

African (AFR)

AF:

0.276

AC:

11451

AN:

41524

American (AMR)

AF:

0.0599

AC:

915

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.00518

AC:

AN:

3472

East Asian (EAS)

AF:

0.0212

AC:

110

AN:

5190

South Asian (SAS)

AF:

0.0314

AC:

151

AN:

4812

European-Finnish (FIN)

AF:

0.0151

AC:

160

AN:

10610

Middle Eastern (MID)

AF:

0.0782

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0118

AC:

803

AN:

68020

Other (OTH)

AF:

0.0653

AC:

138

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

539

1078

1617

2156

2695

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

134

268

402

536

670

<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:

0.0613

Hom.:

233

Bravo

AF:

0.101

Asia WGS

AF:

0.0470

AC:

163

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

8.5

(source)

DANN

Benign

0.74

PhyloP100

0.84

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over