Genetic Variant ENSG00000237707:n.32G>A (chr1-169104108-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 ENST00000415637.2(ENSG00000237707):n.32G>A 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 0.169 in 152,254 control chromosomes in the GnomAD database, including 2,451 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 0.17 ( 2450 hom., cov: 32)

Exomes 𝑓: 0.14 ( 1 hom. )

Consequence

ENSG00000237707
ENST00000415637.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.381

Publications

20 publications found

Variant links:

Genes affected

ENSG00000237707 (HGNC:):

ENSG00000237707 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000415637.2, 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=-0.71).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000415637.2. 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
	LOC101928596	NR_135799.1		n.-16G>A		upstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000237707	ENST00000415637.2	TSL:2	n.32G>A		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000237707	ENST00000781189.1		n.101+34G>A		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.169

AC:

25650

AN:

152028

Hom.:

2448

Cov.:

show subpopulations

Gnomad AFR

AF:

0.261

Gnomad AMI

AF:

0.0768

Gnomad AMR

AF:

0.160

Gnomad ASJ

AF:

0.203

Gnomad EAS

AF:

0.133

Gnomad SAS

AF:

0.113

Gnomad FIN

AF:

0.157

Gnomad MID

AF:

0.263

Gnomad NFE

AF:

0.122

Gnomad OTH

AF:

0.172

GnomAD4 exome

AF:

0.139

AC:

AN:

108

Hom.:

Cov.:

AF XY:

0.167

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)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.125

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.134

AC:

AN:

Other (OTH)

AF:

0.300

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.567

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.169

AC:

25688

AN:

152146

Hom.:

2450

Cov.:

AF XY:

0.170

AC XY:

12624

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.261

AC:

10822

AN:

41480

American (AMR)

AF:

0.161

AC:

2454

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.203

AC:

703

AN:

3470

East Asian (EAS)

AF:

0.133

AC:

689

AN:

5180

South Asian (SAS)

AF:

0.114

AC:

549

AN:

4826

European-Finnish (FIN)

AF:

0.157

AC:

1660

AN:

10582

Middle Eastern (MID)

AF:

0.262

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.122

AC:

8304

AN:

68012

Other (OTH)

AF:

0.171

AC:

360

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1086

2172

3258

4344

5430

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

260

520

780

1040

1300

<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:

0.140

Hom.:

4486

Bravo

AF:

0.172

Asia WGS

AF:

0.141

AC:

493

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

3.0

(source)

DANN

Benign

0.84

PhyloP100

-0.38

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over