dbSNP rs11682175: ENSG00000293318:n.361-4254T>C (chr2-57760458-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 ENST00000605503.2(ENSG00000293318):n.361-4254T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 152,094 control chromosomes in the GnomAD database, including 12,224 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 0.39 ( 12224 hom., cov: 32)

Consequence

ENSG00000293318
ENST00000605503.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.499

Publications

53 publications found

Variant links:

Genes affected

ENSG00000293318 (HGNC:):

ENSG00000293318 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=-0.84).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000293318	ENST00000605503.2 link	n.361-4254T>C	intron_variant	Intron 1 of 1	4
ENSG00000293611	ENST00000715879.1 link	n.499-13737A>G	intron_variant	Intron 5 of 5
ENSG00000293611	ENST00000715880.1 link	n.162-13737A>G	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.385

AC:

58586

AN:

151976

Hom.:

12224

Cov.:

show subpopulations

Gnomad AFR

AF:

0.218

Gnomad AMI

AF:

0.555

Gnomad AMR

AF:

0.396

Gnomad ASJ

AF:

0.524

Gnomad EAS

AF:

0.385

Gnomad SAS

AF:

0.396

Gnomad FIN

AF:

0.391

Gnomad MID

AF:

0.465

Gnomad NFE

AF:

0.473

Gnomad OTH

AF:

0.420

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

GnomAD4 genome

AF:

0.385

AC:

58596

AN:

152094

Hom.:

12224

Cov.:

AF XY:

0.381

AC XY:

28331

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.217

AC:

9017

AN:

41500

American (AMR)

AF:

0.396

AC:

6046

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.524

AC:

1817

AN:

3470

East Asian (EAS)

AF:

0.386

AC:

1998

AN:

5178

South Asian (SAS)

AF:

0.397

AC:

1913

AN:

4816

European-Finnish (FIN)

AF:

0.391

AC:

4140

AN:

10576

Middle Eastern (MID)

AF:

0.466

AC:

137

AN:

294

European-Non Finnish (NFE)

AF:

0.473

AC:

32147

AN:

67970

Other (OTH)

AF:

0.414

AC:

876

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1746

3492

5239

6985

8731

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

574

1148

1722

2296

2870

<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:

0.444

Hom.:

32690

Bravo

AF:

0.379

Asia WGS

AF:

0.362

AC:

1260

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

4.9

(source)

DANN

Benign

0.46

PhyloP100

0.50

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