Genetic Variant EMBP1:n.391+2197G>C (chr1-121559216-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000458200.2(EMBP1):n.391+2197G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 151,678 control chromosomes in the GnomAD database, including 24,296 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 0.56 ( 24296 hom., cov: 32)

Consequence

EMBP1
ENST00000458200.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.84

Publications

7 publications found

Variant links:

Genes affected

EMBP1 (HGNC:38661): (embigin pseudogene 1)

EMBP1 links:

EMBP1 (HGNC:):

EMBP1 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=-1.0).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EMBP1	NR_003955.1 link	n.624+2197G>C		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
EMBP1	ENST00000458200.2 link	n.391+2197G>C	intron_variant	Intron 3 of 7	6
EMBP1	ENST00000618253.2 link	n.731+2197G>C	intron_variant	Intron 4 of 8	4
EMBP1	ENST00000622787.5 link	n.698+2197G>C	intron_variant	Intron 3 of 7	2

Frequencies

GnomAD3 genomes

AF:

0.565

AC:

85573

AN:

151562

Hom.:

24271

Cov.:

show subpopulations

Gnomad AFR

AF:

0.501

Gnomad AMI

AF:

0.498

Gnomad AMR

AF:

0.578

Gnomad ASJ

AF:

0.542

Gnomad EAS

AF:

0.504

Gnomad SAS

AF:

0.399

Gnomad FIN

AF:

0.646

Gnomad MID

AF:

0.506

Gnomad NFE

AF:

0.606

Gnomad OTH

AF:

0.581

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

GnomAD4 genome

AF:

0.565

AC:

85651

AN:

151678

Hom.:

24296

Cov.:

AF XY:

0.564

AC XY:

41807

AN XY:

74086

show subpopulations

African (AFR)

AF:

0.502

AC:

20745

AN:

41354

American (AMR)

AF:

0.578

AC:

8767

AN:

15164

Ashkenazi Jewish (ASJ)

AF:

0.542

AC:

1881

AN:

3468

East Asian (EAS)

AF:

0.504

AC:

2597

AN:

5156

South Asian (SAS)

AF:

0.400

AC:

1924

AN:

4812

European-Finnish (FIN)

AF:

0.646

AC:

6813

AN:

10552

Middle Eastern (MID)

AF:

0.507

AC:

149

AN:

294

European-Non Finnish (NFE)

AF:

0.606

AC:

41108

AN:

67864

Other (OTH)

AF:

0.577

AC:

1215

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1906

3811

5717

7622

9528

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

736

1472

2208

2944

3680

<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:

0.465

Hom.:

1282

Bravo

AF:

0.565

Asia WGS

AF:

0.443

AC:

1544

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.011

(source)

DANN

Benign

0.69

PhyloP100

-4.8

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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