Genetic Variant ENST00000377435.8:n.167G>A (chr2-79137337-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000377435.8(ENSG00000290771):n.167G>A variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0427 in 500,628 control chromosomes in the GnomAD database, including 751 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 0.039 ( 174 hom., cov: 32)

Exomes 𝑓: 0.044 ( 577 hom. )

Consequence

ENSG00000290771
ENST00000377435.8 splice_region, non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0690

Publications

4 publications found

Variant links:

Genes affected

ENSG00000290771 (HGNC:):

ENSG00000290771 links:

REG1CP (HGNC:9953): (regenerating family member 1 gamma, pseudogene)

REG1CP links:

Genome browser will be placed here

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=-0.84).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0585 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
REG1CP	NR_002714.1 link	n.1091G>A		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000290771	ENST00000377435.8 link	n.167G>A	splice_region_variant, non_coding_transcript_exon_variant	Exon 3 of 4	1
ENSG00000290771	ENST00000444841.5 link	n.172G>A	non_coding_transcript_exon_variant	Exon 3 of 4	1
ENSG00000290771	ENST00000414597.6 link	n.404G>A	splice_region_variant, non_coding_transcript_exon_variant	Exon 2 of 5	2

Frequencies

GnomAD3 genomes

AF:

0.0389

AC:

5914

AN:

152100

Hom.:

173

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0113

Gnomad AMI

AF:

0.0505

Gnomad AMR

AF:

0.0455

Gnomad ASJ

AF:

0.0704

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00807

Gnomad FIN

AF:

0.0200

Gnomad MID

AF:

0.0759

Gnomad NFE

AF:

0.0600

Gnomad OTH

AF:

0.0498

GnomAD4 exome

AF:

0.0444

AC:

15452

AN:

348410

Hom.:

577

Cov.:

AF XY:

0.0431

AC XY:

8581

AN XY:

199106

show subpopulations

African (AFR)

AF:

0.0137

AC:

131

AN:

9596

American (AMR)

AF:

0.0307

AC:

984

AN:

32092

Ashkenazi Jewish (ASJ)

AF:

0.0811

AC:

778

AN:

9594

East Asian (EAS)

AF:

0.00

AC:

AN:

13166

South Asian (SAS)

AF:

0.00861

AC:

536

AN:

62226

European-Finnish (FIN)

AF:

0.0269

AC:

654

AN:

24304

Middle Eastern (MID)

AF:

0.0915

AC:

237

AN:

2590

European-Non Finnish (NFE)

AF:

0.0633

AC:

11364

AN:

179388

Other (OTH)

AF:

0.0497

AC:

768

AN:

15454

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.638

Heterozygous variant carriers

562

1124

1685

2247

2809

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

108

162

216

270

<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:

0.0388

AC:

5908

AN:

152218

Hom.:

174

Cov.:

AF XY:

0.0376

AC XY:

2796

AN XY:

74440

show subpopulations

African (AFR)

AF:

0.0112

AC:

465

AN:

41520

American (AMR)

AF:

0.0455

AC:

696

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0704

AC:

244

AN:

3464

East Asian (EAS)

AF:

0.00

AC:

AN:

5164

South Asian (SAS)

AF:

0.00787

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.0200

AC:

212

AN:

10622

Middle Eastern (MID)

AF:

0.0680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0600

AC:

4083

AN:

68014

Other (OTH)

AF:

0.0492

AC:

104

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

293

586

878

1171

1464

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

136

204

272

340

<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:

0.0446

Hom.:

113

Bravo

AF:

0.0400

Asia WGS

AF:

0.00606

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

3.0

(source)

DANN

Benign

0.41

PhyloP100

-0.069

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over