dbSNP rs439825: ENSG00000291003:n.3523G>A (chr15-22561372-G-A) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000619021.5(ENSG00000291003):n.3523G>A variant causes a non coding transcript exon change. 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 0.00011 ( 0 hom., cov: 21)

Exomes 𝑓: 0.000068 ( 36 hom. )

Failed GnomAD Quality Control

Consequence

ENSG00000291003
ENST00000619021.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.80

Publications

1 publications found

Variant links:

Genes affected

ENSG00000291003 (HGNC:):

ENSG00000291003 links:

HERC2P2 (HGNC:4870): (HERC2 pseudogene 2)

HERC2P2 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000619021.5, 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: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.48).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000619021.5. 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
	HERC2P2	NR_002824.3		n.3412G>A		non_coding_transcript_exon	Exon 22 of 35

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
ENSG00000291003	ENST00000619021.5	TSL:1	n.3523G>A	non_coding_transcript_exon	Exon 23 of 35
HERC2P2	ENST00000613386.4	TSL:6	n.3293G>A	non_coding_transcript_exon	Exon 21 of 32
ENSG00000291003	ENST00000835776.1		n.1090G>A	non_coding_transcript_exon	Exon 4 of 6

Frequencies

GnomAD3 genomes

AF:

0.000122

AC:

AN:

131250

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000924

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000757

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000204

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000103

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000147

Gnomad OTH

AF:

0.000579

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000682

AC:

AN:

1334258

Hom.:

Cov.:

AF XY:

0.0000872

AC XY:

AN XY:

665134

show subpopulations

African (AFR)

AF:

0.000210

AC:

AN:

28544

American (AMR)

AF:

0.000309

AC:

AN:

42090

Ashkenazi Jewish (ASJ)

AF:

0.0000432

AC:

AN:

23172

East Asian (EAS)

AF:

0.00

AC:

AN:

39308

South Asian (SAS)

AF:

0.000338

AC:

AN:

76836

European-Finnish (FIN)

AF:

0.0000387

AC:

AN:

51688

Middle Eastern (MID)

AF:

0.000574

AC:

AN:

3482

European-Non Finnish (NFE)

AF:

0.0000315

AC:

AN:

1014292

Other (OTH)

AF:

0.000164

AC:

AN:

54846

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.462

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000114

AC:

AN:

131342

Hom.:

Cov.:

AF XY:

0.0000939

AC XY:

AN XY:

63876

show subpopulations

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.0000921

AC:

AN:

32570

American (AMR)

AF:

0.0000756

AC:

AN:

13224

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2928

East Asian (EAS)

AF:

0.00

AC:

AN:

4880

South Asian (SAS)

AF:

0.00

AC:

AN:

3806

European-Finnish (FIN)

AF:

0.000103

AC:

AN:

9722

Middle Eastern (MID)

AF:

0.00

AC:

AN:

232

European-Non Finnish (NFE)

AF:

0.000147

AC:

AN:

61424

Other (OTH)

AF:

0.000572

AC:

AN:

1748

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.266

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome 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

Alfa

AF:

0.00101

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.48

CADD

Benign

(source)

DANN

Benign

0.75

PhyloP100

6.8

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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