dbSNP rs7600259: ENSG00000226994:n.180+36734T>G (chr2-34868226-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000453451.5(ENSG00000226994):n.180+36734T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,192 control chromosomes in the GnomAD database, including 1,119 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 0.12 ( 1119 hom., cov: 32)

Consequence

ENSG00000226994
ENST00000453451.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.73

Publications

3 publications found

Variant links:

Genes affected

ENSG00000226994 (HGNC:):

ENSG00000226994 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=-0.51).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.129 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
ENSG00000226994	ENST00000453451.5 link	n.180+36734T>G	intron_variant	Intron 2 of 5	4
ENSG00000226994	ENST00000585391.6 link	n.115+36734T>G	intron_variant	Intron 1 of 6	5
ENSG00000226994	ENST00000586769.6 link	n.157+36734T>G	intron_variant	Intron 1 of 5	5

Frequencies

GnomAD3 genomes

AF:

0.121

AC:

18468

AN:

152074

Hom.:

1117

Cov.:

show subpopulations

Gnomad AFR

AF:

0.132

Gnomad AMI

AF:

0.101

Gnomad AMR

AF:

0.0923

Gnomad ASJ

AF:

0.179

Gnomad EAS

AF:

0.117

Gnomad SAS

AF:

0.113

Gnomad FIN

AF:

0.111

Gnomad MID

AF:

0.136

Gnomad NFE

AF:

0.121

Gnomad OTH

AF:

0.119

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

GnomAD4 genome

AF:

0.121

AC:

18478

AN:

152192

Hom.:

1119

Cov.:

AF XY:

0.120

AC XY:

8900

AN XY:

74404

show subpopulations

African (AFR)

AF:

0.132

AC:

5495

AN:

41536

American (AMR)

AF:

0.0922

AC:

1409

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.179

AC:

620

AN:

3466

East Asian (EAS)

AF:

0.117

AC:

608

AN:

5178

South Asian (SAS)

AF:

0.112

AC:

542

AN:

4830

European-Finnish (FIN)

AF:

0.111

AC:

1174

AN:

10614

Middle Eastern (MID)

AF:

0.136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.121

AC:

8247

AN:

67978

Other (OTH)

AF:

0.119

AC:

251

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

840

1681

2521

3362

4202

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

202

404

606

808

1010

<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:

0.122

Hom.:

5111

Bravo

AF:

0.121

Asia WGS

AF:

0.108

AC:

375

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

CADD

Benign

(source)

DANN

Benign

0.79

PhyloP100

2.7

Mutation Taster

=100/0

polymorphism

(source)

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