Genetic Variant ENST00000847198.1:n.176-20385G>C (chr2-185199269-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 ENST00000847198.1(ENSG00000310103):n.176-20385G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 151,042 control chromosomes in the GnomAD database, including 8,304 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 0.32 ( 8304 hom., cov: 32)

Consequence

ENSG00000310103
ENST00000847198.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.74

Publications

3 publications found

Variant links:

Genes affected

ENSG00000310103 (HGNC:):

ENSG00000310103 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=-0.95).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105373781	XR_923661.1 link	n.363+2504G>C	intron_variant	Intron 3 of 4
LOC105373781	XR_923662.1 link	n.333+2504G>C	intron_variant	Intron 3 of 4
LOC105373781	XR_923663.1 link	n.215-20385G>C	intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310103	ENST00000847198.1 link	n.176-20385G>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.325

AC:

48998

AN:

150926

Hom.:

8282

Cov.:

show subpopulations

Gnomad AFR

AF:

0.251

Gnomad AMI

AF:

0.541

Gnomad AMR

AF:

0.252

Gnomad ASJ

AF:

0.326

Gnomad EAS

AF:

0.404

Gnomad SAS

AF:

0.478

Gnomad FIN

AF:

0.392

Gnomad MID

AF:

0.250

Gnomad NFE

AF:

0.357

Gnomad OTH

AF:

0.310

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

GnomAD4 genome

AF:

0.325

AC:

49055

AN:

151042

Hom.:

8304

Cov.:

AF XY:

0.326

AC XY:

24031

AN XY:

73768

show subpopulations

African (AFR)

AF:

0.251

AC:

10364

AN:

41334

American (AMR)

AF:

0.252

AC:

3811

AN:

15114

Ashkenazi Jewish (ASJ)

AF:

0.326

AC:

1123

AN:

3450

East Asian (EAS)

AF:

0.404

AC:

2070

AN:

5122

South Asian (SAS)

AF:

0.480

AC:

2311

AN:

4816

European-Finnish (FIN)

AF:

0.392

AC:

4091

AN:

10442

Middle Eastern (MID)

AF:

0.231

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.357

AC:

24057

AN:

67460

Other (OTH)

AF:

0.318

AC:

668

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1683

3366

5048

6731

8414

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

502

1004

1506

2008

2510

<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:

0.336

Hom.:

1093

Bravo

AF:

0.311

Asia WGS

AF:

0.453

AC:

1552

AN:

3436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.015

(source)

DANN

Benign

0.48

PhyloP100

-1.7

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