dbSNP rs947425: ENSG00000227712:n.341+6230C>T (chr1-119320733-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000457719.1(ENSG00000227712):n.341+6230C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,100 control chromosomes in the GnomAD database, including 2,166 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 0.10 ( 2166 hom., cov: 32)

Consequence

ENSG00000227712
ENST00000457719.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.378

Publications

2 publications found

Variant links:

Genes affected

ENSG00000227712 (HGNC:):

ENSG00000227712 links:

WARS2-AS1 (HGNC:40612): (WARS2 antisense RNA 1)

WARS2-AS1 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=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.303 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
ENSG00000227712	ENST00000457719.1 link	n.341+6230C>T	intron_variant	Intron 1 of 2	2
ENSG00000227712	ENST00000653227.2 link	n.308-2806C>T	intron_variant	Intron 2 of 2
ENSG00000227712	ENST00000655614.1 link	n.254+6230C>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.103

AC:

15633

AN:

151980

Hom.:

2156

Cov.:

show subpopulations

Gnomad AFR

AF:

0.307

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0418

Gnomad ASJ

AF:

0.0153

Gnomad EAS

AF:

0.134

Gnomad SAS

AF:

0.0628

Gnomad FIN

AF:

0.0356

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0101

Gnomad OTH

AF:

0.0813

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

GnomAD4 genome

AF:

0.103

AC:

15675

AN:

152100

Hom.:

2166

Cov.:

AF XY:

0.103

AC XY:

7657

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.307

AC:

12738

AN:

41448

American (AMR)

AF:

0.0418

AC:

638

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.0153

AC:

AN:

3472

East Asian (EAS)

AF:

0.134

AC:

692

AN:

5170

South Asian (SAS)

AF:

0.0622

AC:

300

AN:

4822

European-Finnish (FIN)

AF:

0.0356

AC:

377

AN:

10588

Middle Eastern (MID)

AF:

0.0306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0101

AC:

690

AN:

68008

Other (OTH)

AF:

0.0843

AC:

178

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

570

1140

1711

2281

2851

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

148

296

444

592

740

<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:

0.0380

Hom.:

2303

Bravo

AF:

0.111

Asia WGS

AF:

0.149

AC:

517

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.28

(source)

DANN

Benign

0.62

PhyloP100

-0.38

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