Genetic Variant ENSG00000226334:n.1164+5348T>C (chr9-104933258-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 ENST00000820514.1(ENSG00000226334):n.1164+5348T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.609 in 152,052 control chromosomes in the GnomAD database, including 28,385 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 0.61 ( 28385 hom., cov: 32)

Consequence

ENSG00000226334
ENST00000820514.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.96

Publications

16 publications found

Variant links:

COSMIC-nc: COSV71347137

Genes affected

ENSG00000226334 (HGNC:):

ENSG00000226334 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=-1.01).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376196	NR_188620.1 link	n.1339+3534T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226334	ENST00000820514.1 link	n.1164+5348T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.609

AC:

92496

AN:

151934

Hom.:

28368

Cov.:

show subpopulations

Gnomad AFR

AF:

0.645

Gnomad AMI

AF:

0.702

Gnomad AMR

AF:

0.648

Gnomad ASJ

AF:

0.700

Gnomad EAS

AF:

0.463

Gnomad SAS

AF:

0.674

Gnomad FIN

AF:

0.627

Gnomad MID

AF:

0.687

Gnomad NFE

AF:

0.576

Gnomad OTH

AF:

0.602

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

GnomAD4 genome

AF:

0.609

AC:

92556

AN:

152052

Hom.:

28385

Cov.:

AF XY:

0.612

AC XY:

45469

AN XY:

74312

show subpopulations

African (AFR)

AF:

0.645

AC:

26745

AN:

41478

American (AMR)

AF:

0.649

AC:

9900

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.700

AC:

2431

AN:

3472

East Asian (EAS)

AF:

0.463

AC:

2392

AN:

5168

South Asian (SAS)

AF:

0.674

AC:

3249

AN:

4824

European-Finnish (FIN)

AF:

0.627

AC:

6621

AN:

10564

Middle Eastern (MID)

AF:

0.694

AC:

204

AN:

294

European-Non Finnish (NFE)

AF:

0.576

AC:

39127

AN:

67974

Other (OTH)

AF:

0.592

AC:

1250

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1886

3772

5658

7544

9430

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

762

1524

2286

3048

3810

<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:

0.590

Hom.:

3168

Bravo

AF:

0.611

Asia WGS

AF:

0.557

AC:

1936

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.91

(source)

DANN

Benign

0.68

PhyloP100

-2.0

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