dbSNP rs1041163: ENSG00000299357:n.154+17415A>G (chr1-100718269-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 ENST00000762830.1(ENSG00000299357):n.154+17415A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,134 control chromosomes in the GnomAD database, including 2,603 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 0.18 ( 2603 hom., cov: 32)

Consequence

ENSG00000299357
ENST00000762830.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.312

Publications

49 publications found

Variant links:

Genes affected

ENSG00000299357 (HGNC:):

ENSG00000299357 links:

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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=-0.81).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.267 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
ENSG00000299357	ENST00000762830.1 link	n.154+17415A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.177

AC:

26895

AN:

152016

Hom.:

2598

Cov.:

show subpopulations

Gnomad AFR

AF:

0.181

Gnomad AMI

AF:

0.179

Gnomad AMR

AF:

0.273

Gnomad ASJ

AF:

0.287

Gnomad EAS

AF:

0.145

Gnomad SAS

AF:

0.143

Gnomad FIN

AF:

0.145

Gnomad MID

AF:

0.212

Gnomad NFE

AF:

0.155

Gnomad OTH

AF:

0.225

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

GnomAD4 genome

AF:

0.177

AC:

26914

AN:

152134

Hom.:

2603

Cov.:

AF XY:

0.176

AC XY:

13104

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.181

AC:

7525

AN:

41510

American (AMR)

AF:

0.274

AC:

4179

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.287

AC:

997

AN:

3472

East Asian (EAS)

AF:

0.145

AC:

749

AN:

5160

South Asian (SAS)

AF:

0.142

AC:

684

AN:

4822

European-Finnish (FIN)

AF:

0.145

AC:

1539

AN:

10598

Middle Eastern (MID)

AF:

0.201

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.155

AC:

10549

AN:

67986

Other (OTH)

AF:

0.222

AC:

470

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1112

2223

3335

4446

5558

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

288

576

864

1152

1440

<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:

0.168

Hom.:

9647

Bravo

AF:

0.191

Asia WGS

AF:

0.143

AC:

500

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

(source)

DANN

Benign

0.75

PhyloP100

0.31

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