dbSNP rs4561414: ENSG00000309432:n.326+8969C>T (chr15-95629095-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 ENST00000841104.1(ENSG00000309432):n.326+8969C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,110 control chromosomes in the GnomAD database, including 1,076 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 ( 1076 hom., cov: 32)

Consequence

ENSG00000309432
ENST00000841104.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.275

Publications

3 publications found

Variant links:

Genes affected

ENSG00000309432 (HGNC:):

ENSG00000309432 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=-0.67).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000309432	ENST00000841104.1 link	n.326+8969C>T	intron_variant	Intron 2 of 4
ENSG00000309432	ENST00000841105.1 link	n.206+8969C>T	intron_variant	Intron 1 of 3
ENSG00000309432	ENST00000841106.1 link	n.208+8969C>T	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.109

AC:

16617

AN:

151992

Hom.:

1072

Cov.:

show subpopulations

Gnomad AFR

AF:

0.163

Gnomad AMI

AF:

0.0121

Gnomad AMR

AF:

0.118

Gnomad ASJ

AF:

0.135

Gnomad EAS

AF:

0.206

Gnomad SAS

AF:

0.0852

Gnomad FIN

AF:

0.0498

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.0778

Gnomad OTH

AF:

0.122

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

GnomAD4 genome

AF:

0.109

AC:

16637

AN:

152110

Hom.:

1076

Cov.:

AF XY:

0.110

AC XY:

8152

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.163

AC:

6777

AN:

41490

American (AMR)

AF:

0.118

AC:

1796

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.135

AC:

468

AN:

3466

East Asian (EAS)

AF:

0.206

AC:

1065

AN:

5166

South Asian (SAS)

AF:

0.0863

AC:

416

AN:

4822

European-Finnish (FIN)

AF:

0.0498

AC:

528

AN:

10592

Middle Eastern (MID)

AF:

0.112

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0778

AC:

5290

AN:

67990

Other (OTH)

AF:

0.120

AC:

253

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

744

1488

2232

2976

3720

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:

0.0901

Hom.:

1237

Bravo

AF:

0.120

Asia WGS

AF:

0.102

AC:

354

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

(source)

DANN

Benign

0.52

PhyloP100

0.28

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