dbSNP rs73511817: ENSG00000307437:n.98-8149G>T (chr9-108383745-C-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000826308.1(ENSG00000307437):n.98-8149G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0421 in 152,028 control chromosomes in the GnomAD database, including 185 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 0.042 ( 185 hom., cov: 32)

Consequence

ENSG00000307437
ENST00000826308.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.84

Publications

0 publications found

Variant links:

Genes affected

ENSG00000307437 (HGNC:):

ENSG00000307437 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.45).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105376214	XR_001746881.2 link	n.326-8149G>T	intron_variant	Intron 1 of 4
LOC105376214	XR_001746882.2 link	n.326-8149G>T	intron_variant	Intron 1 of 5
LOC105376214	XR_007061722.1 link	n.326-8149G>T	intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307437	ENST00000826308.1 link	n.98-8149G>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.0421

AC:

6394

AN:

151910

Hom.:

185

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0686

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0372

Gnomad ASJ

AF:

0.0525

Gnomad EAS

AF:

0.000577

Gnomad SAS

AF:

0.0748

Gnomad FIN

AF:

0.0204

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.0313

Gnomad OTH

AF:

0.0411

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

GnomAD4 genome

AF:

0.0421

AC:

6401

AN:

152028

Hom.:

185

Cov.:

AF XY:

0.0429

AC XY:

3186

AN XY:

74312

show subpopulations

African (AFR)

AF:

0.0686

AC:

2843

AN:

41434

American (AMR)

AF:

0.0371

AC:

566

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.0525

AC:

182

AN:

3468

East Asian (EAS)

AF:

0.000771

AC:

AN:

5190

South Asian (SAS)

AF:

0.0752

AC:

362

AN:

4812

European-Finnish (FIN)

AF:

0.0204

AC:

215

AN:

10560

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0313

AC:

2129

AN:

67970

Other (OTH)

AF:

0.0407

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

329

657

986

1314

1643

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

156

234

312

390

<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:

0.0339

Hom.:

146

Bravo

AF:

0.0432

Asia WGS

AF:

0.0280

AC:

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.45

CADD

Benign

(source)

DANN

Benign

0.55

PhyloP100

1.8

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