Genetic Variant ENSG00000296241:n.436-6178A>G (chr2-210752170-A-G) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000737540.1(ENSG00000296241):n.436-6178A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,138 control chromosomes in the GnomAD database, including 2,125 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 0.15 ( 2125 hom., cov: 32)

Consequence

ENSG00000296241
ENST00000737540.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.531

Publications

31 publications found

Variant links:

Genes affected

ENSG00000296241 (HGNC:):

ENSG00000296241 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.31).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296241	ENST00000737540.1 link	n.436-6178A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.148

AC:

22553

AN:

152020

Hom.:

2121

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0335

Gnomad AMI

AF:

0.198

Gnomad AMR

AF:

0.200

Gnomad ASJ

AF:

0.161

Gnomad EAS

AF:

0.155

Gnomad SAS

AF:

0.187

Gnomad FIN

AF:

0.287

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.181

Gnomad OTH

AF:

0.142

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

GnomAD4 genome

AF:

0.148

AC:

22554

AN:

152138

Hom.:

2125

Cov.:

AF XY:

0.155

AC XY:

11501

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.0334

AC:

1386

AN:

41536

American (AMR)

AF:

0.200

AC:

3050

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.161

AC:

557

AN:

3468

East Asian (EAS)

AF:

0.155

AC:

801

AN:

5166

South Asian (SAS)

AF:

0.188

AC:

908

AN:

4826

European-Finnish (FIN)

AF:

0.287

AC:

3031

AN:

10564

Middle Eastern (MID)

AF:

0.0952

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.181

AC:

12315

AN:

67980

Other (OTH)

AF:

0.141

AC:

297

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

940

1880

2820

3760

4700

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

262

524

786

1048

1310

<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:

0.166

Hom.:

6736

Bravo

AF:

0.137

Asia WGS

AF:

0.155

AC:

540

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.31

CADD

Benign

(source)

DANN

Benign

0.82

PhyloP100

0.53

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