Genetic Variant ENSG00000286625:n.124+3644T>C (chr5-25967594-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 ENST00000658114.2(ENSG00000286625):n.124+3644T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 152,054 control chromosomes in the GnomAD database, including 7,337 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 0.28 ( 7337 hom., cov: 32)

Consequence

ENSG00000286625
ENST00000658114.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.195

Publications

77 publications found

Variant links:

Genes affected

ENSG00000286625 (HGNC:):

ENSG00000286625 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=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901176	XR_007059127.1 link	n.58+3644T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000286625	ENST00000658114.2 link	n.124+3644T>C	intron_variant	Intron 1 of 1
ENSG00000286625	ENST00000668718.1 link	n.49+3644T>C	intron_variant	Intron 1 of 1
ENSG00000286625	ENST00000759668.1 link	n.115+3644T>C	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.276

AC:

41878

AN:

151936

Hom.:

7336

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0697

Gnomad AMI

AF:

0.357

Gnomad AMR

AF:

0.268

Gnomad ASJ

AF:

0.457

Gnomad EAS

AF:

0.152

Gnomad SAS

AF:

0.309

Gnomad FIN

AF:

0.419

Gnomad MID

AF:

0.430

Gnomad NFE

AF:

0.376

Gnomad OTH

AF:

0.300

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

GnomAD4 genome

AF:

0.275

AC:

41884

AN:

152054

Hom.:

7337

Cov.:

AF XY:

0.278

AC XY:

20639

AN XY:

74324

show subpopulations

African (AFR)

AF:

0.0696

AC:

2892

AN:

41528

American (AMR)

AF:

0.268

AC:

4086

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.457

AC:

1585

AN:

3472

East Asian (EAS)

AF:

0.152

AC:

785

AN:

5162

South Asian (SAS)

AF:

0.311

AC:

1499

AN:

4818

European-Finnish (FIN)

AF:

0.419

AC:

4424

AN:

10570

Middle Eastern (MID)

AF:

0.425

AC:

125

AN:

294

European-Non Finnish (NFE)

AF:

0.376

AC:

25531

AN:

67944

Other (OTH)

AF:

0.300

AC:

634

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1442

2884

4327

5769

7211

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

438

876

1314

1752

2190

<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:

0.341

Hom.:

31736

Bravo

AF:

0.256

Asia WGS

AF:

0.240

AC:

835

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

4.2

(source)

DANN

Benign

0.55

PhyloP100

0.20

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