dbSNP rs12701220: CHLSN:c.565-4031A>G (chr7-983092-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001424325.1(CHLSN):c.565-4031A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 874,072 control chromosomes in the GnomAD database, including 19,299 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 0.18 ( 2709 hom., cov: 30)

Exomes 𝑓: 0.20 ( 16590 hom. )

Consequence

CHLSN
NM_001424325.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.118

Publications

15 publications found

Variant links:

Genes affected

CHLSN (HGNC:22421): (chromosome 7 open reading frame 50) Enables RNA binding activity. [provided by Alliance of Genome Resources, Apr 2022]

CHLSN links:

ENSG00000310291 (HGNC:):

ENSG00000310291 links:

CYP2W1 (HGNC:20243): (cytochrome P450 family 2 subfamily W member 1) This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. [provided by RefSeq, Jul 2008]

CYP2W1 links:

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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=-0.76).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001424325.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank	Protein
CHLSN	NM_001424325.1	c.565-4031A>G	intron	N/A	NP_001411254.1
CHLSN	NM_001424326.1	c.565-4031A>G	intron	N/A	NP_001411255.1
CHLSN	NM_001424327.1	c.178-3039A>G	intron	N/A	NP_001411256.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000310291	ENST00000848853.1		n.141-4031A>G		intron	N/A
	CYP2W1	ENST00000308919.12	TSL:1 MANE Select	c.-120T>C		upstream_gene	N/A	ENSP00000310149.7	Q8TAV3

Frequencies

GnomAD3 genomes

AF:

0.176

AC:

26268

AN:

149412

Hom.:

2701

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0818

Gnomad AMI

AF:

0.180

Gnomad AMR

AF:

0.222

Gnomad ASJ

AF:

0.115

Gnomad EAS

AF:

0.304

Gnomad SAS

AF:

0.142

Gnomad FIN

AF:

0.291

Gnomad MID

AF:

0.128

Gnomad NFE

AF:

0.202

Gnomad OTH

AF:

0.172

GnomAD4 exome

AF:

0.205

AC:

148497

AN:

724540

Hom.:

16590

AF XY:

0.203

AC XY:

72600

AN XY:

358300

show subpopulations

African (AFR)

AF:

0.0723

AC:

1128

AN:

15606

American (AMR)

AF:

0.256

AC:

3154

AN:

12336

Ashkenazi Jewish (ASJ)

AF:

0.108

AC:

1414

AN:

13136

East Asian (EAS)

AF:

0.354

AC:

9175

AN:

25920

South Asian (SAS)

AF:

0.142

AC:

4512

AN:

31752

European-Finnish (FIN)

AF:

0.283

AC:

7695

AN:

27176

Middle Eastern (MID)

AF:

0.126

AC:

293

AN:

2324

European-Non Finnish (NFE)

AF:

0.204

AC:

115184

AN:

563434

Other (OTH)

AF:

0.181

AC:

5942

AN:

32856

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

5991

11982

17973

23964

29955

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3772

7544

11316

15088

18860

<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:

0.176

AC:

26289

AN:

149532

Hom.:

2709

Cov.:

AF XY:

0.178

AC XY:

13007

AN XY:

72992

show subpopulations

African (AFR)

AF:

0.0817

AC:

3350

AN:

40984

American (AMR)

AF:

0.222

AC:

3366

AN:

15154

Ashkenazi Jewish (ASJ)

AF:

0.115

AC:

396

AN:

3436

East Asian (EAS)

AF:

0.306

AC:

1506

AN:

4926

South Asian (SAS)

AF:

0.143

AC:

658

AN:

4612

European-Finnish (FIN)

AF:

0.291

AC:

2935

AN:

10094

Middle Eastern (MID)

AF:

0.134

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.202

AC:

13526

AN:

67056

Other (OTH)

AF:

0.169

AC:

351

AN:

2080

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1017

2035

3052

4070

5087

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

284

568

852

1136

1420

<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:

0.185

Hom.:

3899

Bravo

AF:

0.169

Asia WGS

AF:

0.197

AC:

684

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

7.3

(source)

DANN

Benign

0.66

PhyloP100

0.12

PromoterAI

-0.054

Neutral

(source)

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over