dbSNP rs10493513: ENSG00000298890:n.99-3197G>A (chr1-72913906-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is . The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000758621.1(ENSG00000298890):n.99-3197G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 151,808 control chromosomes in the GnomAD database, including 13,375 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 0.38 ( 13375 hom., cov: 32)

Consequence

ENSG00000298890
ENST00000758621.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.100

Publications

3 publications found

Variant links:

Genes affected

ENSG00000298890 (HGNC:):

ENSG00000298890 links:

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new If you want to explore the variant's impact on the transcript ENST00000758621.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000758621.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298890	ENST00000758621.1		n.99-3197G>A		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.380

AC:

57705

AN:

151690

Hom.:

13385

Cov.:

show subpopulations

Gnomad AFR

AF:

0.116

Gnomad AMI

AF:

0.465

Gnomad AMR

AF:

0.496

Gnomad ASJ

AF:

0.484

Gnomad EAS

AF:

0.171

Gnomad SAS

AF:

0.381

Gnomad FIN

AF:

0.552

Gnomad MID

AF:

0.408

Gnomad NFE

AF:

0.498

Gnomad OTH

AF:

0.385

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

GnomAD4 genome

AF:

0.380

AC:

57700

AN:

151808

Hom.:

13375

Cov.:

AF XY:

0.383

AC XY:

28434

AN XY:

74180

show subpopulations

African (AFR)

AF:

0.116

AC:

4814

AN:

41458

American (AMR)

AF:

0.495

AC:

7528

AN:

15204

Ashkenazi Jewish (ASJ)

AF:

0.484

AC:

1679

AN:

3470

East Asian (EAS)

AF:

0.171

AC:

879

AN:

5138

South Asian (SAS)

AF:

0.382

AC:

1842

AN:

4822

European-Finnish (FIN)

AF:

0.552

AC:

5809

AN:

10532

Middle Eastern (MID)

AF:

0.412

AC:

121

AN:

294

European-Non Finnish (NFE)

AF:

0.498

AC:

33803

AN:

67882

Other (OTH)

AF:

0.382

AC:

804

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1591

3183

4774

6366

7957

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

542

1084

1626

2168

2710

<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:

0.428

Hom.:

2075

Bravo

AF:

0.366

Asia WGS

AF:

0.261

AC:

908

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.28

(source)

DANN

Benign

0.36

PhyloP100

0.10

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over