dbSNP rs1071882: ENSG00000285978:n.257-1867G>A (chr5-178709039-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000638723.1(ENSG00000285978):n.257-1867G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,120 control chromosomes in the GnomAD database, including 5,214 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 0.25 ( 5214 hom., cov: 33)

Consequence

ENSG00000285978
ENST00000638723.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.776

Publications

5 publications found

Variant links:

COSMIC-nc: COSV59982538

Genes affected

ENSG00000285978 (HGNC:):

ENSG00000285978 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=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.379 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
ENSG00000285978	ENST00000638723.1 link	n.257-1867G>A		intron_variant	Intron 3 of 7	5		ENSP00000492050.1		A0A1W2PQE6

Frequencies

GnomAD3 genomes

AF:

0.250

AC:

37988

AN:

152002

Hom.:

5209

Cov.:

show subpopulations

Gnomad AFR

AF:

0.137

Gnomad AMI

AF:

0.158

Gnomad AMR

AF:

0.248

Gnomad ASJ

AF:

0.285

Gnomad EAS

AF:

0.330

Gnomad SAS

AF:

0.393

Gnomad FIN

AF:

0.387

Gnomad MID

AF:

0.288

Gnomad NFE

AF:

0.281

Gnomad OTH

AF:

0.240

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

GnomAD4 genome

AF:

0.250

AC:

38019

AN:

152120

Hom.:

5214

Cov.:

AF XY:

0.258

AC XY:

19196

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.138

AC:

5708

AN:

41510

American (AMR)

AF:

0.248

AC:

3790

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.285

AC:

988

AN:

3470

East Asian (EAS)

AF:

0.330

AC:

1708

AN:

5176

South Asian (SAS)

AF:

0.394

AC:

1897

AN:

4816

European-Finnish (FIN)

AF:

0.387

AC:

4085

AN:

10566

Middle Eastern (MID)

AF:

0.279

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.281

AC:

19095

AN:

67972

Other (OTH)

AF:

0.247

AC:

522

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

1395

2789

4184

5578

6973

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

404

808

1212

1616

2020

<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:

0.279

Hom.:

3813

Bravo

AF:

0.230

Asia WGS

AF:

0.372

AC:

1296

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.2

(source)

DANN

Benign

0.55

PhyloP100

-0.78

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