dbSNP rs975977: ENSG00000286548:n.258-3351C>T (chr1-89485214-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 ENST00000662176.1(ENSG00000286548):n.258-3351C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,030 control chromosomes in the GnomAD database, including 2,944 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 ( 2944 hom., cov: 32)

Consequence

ENSG00000286548
ENST00000662176.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.852

Publications

1 publications found

Variant links:

COSMIC-nc: COSV59970737

Genes affected

ENSG00000286548 (HGNC:):

ENSG00000286548 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=-0.97).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.291 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
ENSG00000286548	ENST00000662176.1 link	n.258-3351C>T		intron_variant	Intron 1 of 4
ENSG00000286548	ENST00000671515.1 link	n.317-3351C>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes

AF:

0.176

AC:

26800

AN:

151914

Hom.:

2940

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0625

Gnomad AMI

AF:

0.296

Gnomad AMR

AF:

0.297

Gnomad ASJ

AF:

0.191

Gnomad EAS

AF:

0.0210

Gnomad SAS

AF:

0.170

Gnomad FIN

AF:

0.175

Gnomad MID

AF:

0.244

Gnomad NFE

AF:

0.228

Gnomad OTH

AF:

0.190

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

GnomAD4 genome

AF:

0.176

AC:

26807

AN:

152030

Hom.:

2944

Cov.:

AF XY:

0.175

AC XY:

13003

AN XY:

74318

show subpopulations

African (AFR)

AF:

0.0624

AC:

2587

AN:

41476

American (AMR)

AF:

0.298

AC:

4545

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.191

AC:

662

AN:

3468

East Asian (EAS)

AF:

0.0213

AC:

110

AN:

5176

South Asian (SAS)

AF:

0.170

AC:

818

AN:

4820

European-Finnish (FIN)

AF:

0.175

AC:

1842

AN:

10534

Middle Eastern (MID)

AF:

0.241

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.228

AC:

15506

AN:

67980

Other (OTH)

AF:

0.188

AC:

397

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1077

2154

3230

4307

5384

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

284

568

852

1136

1420

<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:

0.202

Hom.:

427

Bravo

AF:

0.181

Asia WGS

AF:

0.100

AC:

350

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.17

(source)

DANN

Benign

0.61

PhyloP100

-0.85

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