dbSNP rs17145184: ENSG00000226829:n.465+8662A>G (chr7-68176128-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 ENST00000446187.2(ENSG00000226829):n.465+8662A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,198 control chromosomes in the GnomAD database, including 2,226 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 0.15 ( 2226 hom., cov: 32)

Consequence

ENSG00000226829
ENST00000446187.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.820

Publications

1 publications found

Variant links:

Genes affected

ENSG00000226829 (HGNC:):

ENSG00000226829 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=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375341	NR_187905.1 link	n.523+8662A>G		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226829	ENST00000446187.2 link	n.465+8662A>G		intron_variant	Intron 4 of 5	5

Frequencies

GnomAD3 genomes

AF:

0.154

AC:

23462

AN:

152080

Hom.:

2204

Cov.:

show subpopulations

Gnomad AFR

AF:

0.260

Gnomad AMI

AF:

0.211

Gnomad AMR

AF:

0.139

Gnomad ASJ

AF:

0.0746

Gnomad EAS

AF:

0.203

Gnomad SAS

AF:

0.174

Gnomad FIN

AF:

0.118

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.0977

Gnomad OTH

AF:

0.139

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

GnomAD4 genome

AF:

0.155

AC:

23534

AN:

152198

Hom.:

2226

Cov.:

AF XY:

0.158

AC XY:

11763

AN XY:

74416

show subpopulations

African (AFR)

AF:

0.261

AC:

10833

AN:

41508

American (AMR)

AF:

0.139

AC:

2120

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.0746

AC:

259

AN:

3472

East Asian (EAS)

AF:

0.203

AC:

1052

AN:

5174

South Asian (SAS)

AF:

0.175

AC:

843

AN:

4826

European-Finnish (FIN)

AF:

0.118

AC:

1253

AN:

10608

Middle Eastern (MID)

AF:

0.109

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0977

AC:

6647

AN:

68008

Other (OTH)

AF:

0.143

AC:

303

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

970

1940

2911

3881

4851

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

252

504

756

1008

1260

<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:

0.115

Hom.:

4724

Bravo

AF:

0.158

Asia WGS

AF:

0.187

AC:

652

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

2.9

(source)

DANN

Benign

0.57

PhyloP100

-0.82

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