Genetic Variant XR_007066136.1:n.4476A>G (chr1-58765488-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The XR_007066136.1(LOC105378751):n.4476A>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 0.568 in 152,076 control chromosomes in the GnomAD database, including 27,678 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 0.57 ( 27678 hom., cov: 32)

Consequence

LOC105378751
XR_007066136.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0100

Publications

7 publications found

Variant links:

Genes affected

LOC105378751 (HGNC:):

LOC105378751 links:

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new If you want to explore the variant's impact on the transcript XR_007066136.1, 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=-0.9).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000636386.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000283445	ENST00000636386.1	TSL:5	n.330-622A>G		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.568

AC:

86282

AN:

151958

Hom.:

27660

Cov.:

show subpopulations

Gnomad AFR

AF:

0.239

Gnomad AMI

AF:

0.844

Gnomad AMR

AF:

0.695

Gnomad ASJ

AF:

0.689

Gnomad EAS

AF:

0.610

Gnomad SAS

AF:

0.666

Gnomad FIN

AF:

0.726

Gnomad MID

AF:

0.617

Gnomad NFE

AF:

0.694

Gnomad OTH

AF:

0.590

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

GnomAD4 genome

AF:

0.568

AC:

86313

AN:

152076

Hom.:

27678

Cov.:

AF XY:

0.573

AC XY:

42586

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.238

AC:

9885

AN:

41488

American (AMR)

AF:

0.695

AC:

10628

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.689

AC:

2390

AN:

3468

East Asian (EAS)

AF:

0.610

AC:

3156

AN:

5172

South Asian (SAS)

AF:

0.665

AC:

3205

AN:

4816

European-Finnish (FIN)

AF:

0.726

AC:

7657

AN:

10552

Middle Eastern (MID)

AF:

0.629

AC:

185

AN:

294

European-Non Finnish (NFE)

AF:

0.694

AC:

47190

AN:

67978

Other (OTH)

AF:

0.591

AC:

1247

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1598

3196

4793

6391

7989

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

714

1428

2142

2856

3570

<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:

0.645

Hom.:

89240

Bravo

AF:

0.552

Asia WGS

AF:

0.614

AC:

2138

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.3

(source)

DANN

Benign

0.63

PhyloP100

0.010

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