dbSNP rs11571300: ENSG00000305408:n.63+1225A>G (chr2-203882044-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000810800.1(ENSG00000305408):n.63+1225A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,132 control chromosomes in the GnomAD database, including 1,093 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 0.11 ( 1093 hom., cov: 32)

Consequence

ENSG00000305408
ENST00000810800.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0500

Publications

9 publications found

Variant links:

Genes affected

ENSG00000305408 (HGNC:):

ENSG00000305408 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=-0.74).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.137 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
ENSG00000305408	ENST00000810800.1 link	n.63+1225A>G		intron_variant	Intron 1 of 2
ENSG00000305408	ENST00000810801.1 link	n.83+1225A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.106

AC:

16185

AN:

152014

Hom.:

1089

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0287

Gnomad AMI

AF:

0.0461

Gnomad AMR

AF:

0.134

Gnomad ASJ

AF:

0.163

Gnomad EAS

AF:

0.123

Gnomad SAS

AF:

0.140

Gnomad FIN

AF:

0.119

Gnomad MID

AF:

0.105

Gnomad NFE

AF:

0.139

Gnomad OTH

AF:

0.132

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

GnomAD4 genome

AF:

0.106

AC:

16189

AN:

152132

Hom.:

1093

Cov.:

AF XY:

0.106

AC XY:

7887

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.0286

AC:

1187

AN:

41524

American (AMR)

AF:

0.134

AC:

2049

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.163

AC:

566

AN:

3470

East Asian (EAS)

AF:

0.123

AC:

637

AN:

5174

South Asian (SAS)

AF:

0.140

AC:

670

AN:

4792

European-Finnish (FIN)

AF:

0.119

AC:

1256

AN:

10576

Middle Eastern (MID)

AF:

0.0993

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.139

AC:

9480

AN:

68000

Other (OTH)

AF:

0.130

AC:

273

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

735

1470

2205

2940

3675

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

182

364

546

728

910

<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:

0.130

Hom.:

1755

Bravo

AF:

0.104

Asia WGS

AF:

0.139

AC:

482

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

1.5

(source)

DANN

Benign

0.71

PhyloP100

-0.050

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