dbSNP rs1921246: ENSG00000287172:n.283-21753T>C (chr2-76482424-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 ENST00000798785.1(ENSG00000287172):n.283-21753T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 152,138 control chromosomes in the GnomAD database, including 1,936 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 0.13 ( 1936 hom., cov: 32)

Consequence

ENSG00000287172
ENST00000798785.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.09

Publications

0 publications found

Variant links:

Genes affected

ENSG00000287172 (HGNC:):

ENSG00000287172 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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.45 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
ENSG00000287172	ENST00000798785.1 link	n.283-21753T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.132

AC:

20139

AN:

152020

Hom.:

1941

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0449

Gnomad AMI

AF:

0.144

Gnomad AMR

AF:

0.146

Gnomad ASJ

AF:

0.194

Gnomad EAS

AF:

0.466

Gnomad SAS

AF:

0.271

Gnomad FIN

AF:

0.0808

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.151

Gnomad OTH

AF:

0.157

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

GnomAD4 genome

AF:

0.132

AC:

20136

AN:

152138

Hom.:

1936

Cov.:

AF XY:

0.134

AC XY:

9934

AN XY:

74372

show subpopulations

African (AFR)

AF:

0.0447

AC:

1856

AN:

41526

American (AMR)

AF:

0.146

AC:

2230

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.194

AC:

674

AN:

3468

East Asian (EAS)

AF:

0.466

AC:

2400

AN:

5152

South Asian (SAS)

AF:

0.272

AC:

1310

AN:

4818

European-Finnish (FIN)

AF:

0.0808

AC:

856

AN:

10588

Middle Eastern (MID)

AF:

0.245

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.151

AC:

10270

AN:

67996

Other (OTH)

AF:

0.159

AC:

337

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

847

1695

2542

3390

4237

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

244

488

732

976

1220

<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:

0.146

Hom.:

985

Bravo

AF:

0.131

Asia WGS

AF:

0.339

AC:

1178

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.18

(source)

DANN

Benign

0.64

PhyloP100

-1.1

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