Genetic Variant ERICH2-DT:n.82+4774A>G (chr2-170808815-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 ENST00000662804.1(ERICH2-DT):n.82+4774A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 152,144 control chromosomes in the GnomAD database, including 4,867 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 0.24 ( 4867 hom., cov: 31)

Consequence

ERICH2-DT
ENST00000662804.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.04

Publications

6 publications found

Variant links:

Genes affected

ERICH2-DT (HGNC:55686): (ERICH2 divergent transcript)

ERICH2-DT links:

ENSG00000295315 (HGNC:):

ENSG00000295315 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 (EAS) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ERICH2-DT	ENST00000662804.1 link	n.82+4774A>G	intron_variant	Intron 1 of 3
ERICH2-DT	ENST00000728834.1 link	n.358+8039A>G	intron_variant	Intron 1 of 4
ERICH2-DT	ENST00000728835.1 link	n.338+8039A>G	intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes

AF:

0.242

AC:

36829

AN:

152026

Hom.:

4863

Cov.:

show subpopulations

Gnomad AFR

AF:

0.195

Gnomad AMI

AF:

0.216

Gnomad AMR

AF:

0.233

Gnomad ASJ

AF:

0.294

Gnomad EAS

AF:

0.576

Gnomad SAS

AF:

0.297

Gnomad FIN

AF:

0.291

Gnomad MID

AF:

0.304

Gnomad NFE

AF:

0.234

Gnomad OTH

AF:

0.247

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

GnomAD4 genome

AF:

0.242

AC:

36833

AN:

152144

Hom.:

4867

Cov.:

AF XY:

0.249

AC XY:

18496

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.194

AC:

8066

AN:

41540

American (AMR)

AF:

0.234

AC:

3568

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.294

AC:

1021

AN:

3470

East Asian (EAS)

AF:

0.577

AC:

2984

AN:

5174

South Asian (SAS)

AF:

0.295

AC:

1422

AN:

4820

European-Finnish (FIN)

AF:

0.291

AC:

3073

AN:

10572

Middle Eastern (MID)

AF:

0.310

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.234

AC:

15888

AN:

67978

Other (OTH)

AF:

0.248

AC:

524

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1389

2778

4166

5555

6944

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.127

Hom.:

218

Bravo

AF:

0.235

Asia WGS

AF:

0.358

AC:

1245

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

6.1

(source)

DANN

Benign

0.80

PhyloP100

1.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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chr2-170808815-T-C

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