Genetic Variant ENSG00000287937:n.223-1186A>G (chr2-112820626-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 ENST00000670671.2(ENSG00000287937):n.223-1186A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 152,150 control chromosomes in the GnomAD database, including 3,697 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 0.22 ( 3697 hom., cov: 32)

Consequence

ENSG00000287937
ENST00000670671.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.246

Publications

12 publications found

Variant links:

Genes affected

ENSG00000287937 (HGNC:):

ENSG00000287937 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 (AFR) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124907871	XR_007087195.1 link	n.220-1186A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000287937	ENST00000670671.2 link	n.223-1186A>G	intron_variant	Intron 1 of 1
ENSG00000299339	ENST00000762706.1 link	n.404+49730T>C	intron_variant	Intron 2 of 3
ENSG00000299339	ENST00000762707.1 link	n.499+49730T>C	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.217

AC:

33059

AN:

152032

Hom.:

3675

Cov.:

show subpopulations

Gnomad AFR

AF:

0.230

Gnomad AMI

AF:

0.325

Gnomad AMR

AF:

0.171

Gnomad ASJ

AF:

0.269

Gnomad EAS

AF:

0.0674

Gnomad SAS

AF:

0.173

Gnomad FIN

AF:

0.246

Gnomad MID

AF:

0.339

Gnomad NFE

AF:

0.225

Gnomad OTH

AF:

0.229

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

GnomAD4 genome

AF:

0.218

AC:

33111

AN:

152150

Hom.:

3697

Cov.:

AF XY:

0.216

AC XY:

16041

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.231

AC:

9588

AN:

41478

American (AMR)

AF:

0.171

AC:

2609

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.269

AC:

935

AN:

3470

East Asian (EAS)

AF:

0.0674

AC:

349

AN:

5178

South Asian (SAS)

AF:

0.174

AC:

837

AN:

4822

European-Finnish (FIN)

AF:

0.246

AC:

2612

AN:

10602

Middle Eastern (MID)

AF:

0.337

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.225

AC:

15302

AN:

68000

Other (OTH)

AF:

0.229

AC:

484

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1351

2703

4054

5406

6757

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

352

704

1056

1408

1760

<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:

0.220

Hom.:

5101

Bravo

AF:

0.210

Asia WGS

AF:

0.131

AC:

456

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

4.3

(source)

DANN

Benign

0.72

PhyloP100

-0.25

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