dbSNP rs9609396: ENSG00000227519:n.59-2212C>T (chr22-31967774-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000430449.1(ENSG00000227519):n.59-2212C>T 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 152,120 control chromosomes in the GnomAD database, including 1,398 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 ( 1398 hom., cov: 31)

Consequence

ENSG00000227519
ENST00000430449.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.168

Publications

6 publications found

Variant links:

Genes affected

ENSG00000227519 (HGNC:):

ENSG00000227519 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 (NFE) allele frequency at 95% confidence interval = 0.161 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
ENSG00000227519	ENST00000430449.1 link	n.59-2212C>T		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes

AF:

0.121

AC:

18334

AN:

152004

Hom.:

1396

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0339

Gnomad AMI

AF:

0.268

Gnomad AMR

AF:

0.119

Gnomad ASJ

AF:

0.145

Gnomad EAS

AF:

0.0867

Gnomad SAS

AF:

0.118

Gnomad FIN

AF:

0.183

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.164

Gnomad OTH

AF:

0.112

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

GnomAD4 genome

AF:

0.121

AC:

18336

AN:

152120

Hom.:

1398

Cov.:

AF XY:

0.122

AC XY:

9100

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.0339

AC:

1406

AN:

41536

American (AMR)

AF:

0.119

AC:

1812

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.145

AC:

505

AN:

3472

East Asian (EAS)

AF:

0.0865

AC:

447

AN:

5166

South Asian (SAS)

AF:

0.119

AC:

575

AN:

4816

European-Finnish (FIN)

AF:

0.183

AC:

1938

AN:

10566

Middle Eastern (MID)

AF:

0.143

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.164

AC:

11131

AN:

67978

Other (OTH)

AF:

0.112

AC:

236

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

813

1625

2438

3250

4063

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

212

424

636

848

1060

<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:

0.147

Hom.:

376

Bravo

AF:

0.111

Asia WGS

AF:

0.0830

AC:

287

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

3.4

(source)

DANN

Benign

0.62

PhyloP100

-0.17

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