dbSNP rs10519980: ENSG00000287292:n.223-152884C>T (chr4-148713873-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 ENST00000661928.1(ENSG00000287292):n.223-152884C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 151,934 control chromosomes in the GnomAD database, including 4,007 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 0.22 ( 4007 hom., cov: 32)

Consequence

ENSG00000287292
ENST00000661928.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.523

Publications

16 publications found

Variant links:

Genes affected

ENSG00000287292 (HGNC:):

ENSG00000287292 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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986195	XR_001741441.2 link	n.3662-152884C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287292	ENST00000661928.1 link	n.223-152884C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.216

AC:

32855

AN:

151818

Hom.:

4008

Cov.:

show subpopulations

Gnomad AFR

AF:

0.330

Gnomad AMI

AF:

0.162

Gnomad AMR

AF:

0.158

Gnomad ASJ

AF:

0.174

Gnomad EAS

AF:

0.0622

Gnomad SAS

AF:

0.149

Gnomad FIN

AF:

0.115

Gnomad MID

AF:

0.229

Gnomad NFE

AF:

0.195

Gnomad OTH

AF:

0.218

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

GnomAD4 genome

AF:

0.216

AC:

32873

AN:

151934

Hom.:

4007

Cov.:

AF XY:

0.210

AC XY:

15579

AN XY:

74236

show subpopulations

African (AFR)

AF:

0.330

AC:

13677

AN:

41426

American (AMR)

AF:

0.158

AC:

2409

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.174

AC:

605

AN:

3472

East Asian (EAS)

AF:

0.0621

AC:

321

AN:

5166

South Asian (SAS)

AF:

0.149

AC:

716

AN:

4818

European-Finnish (FIN)

AF:

0.115

AC:

1213

AN:

10522

Middle Eastern (MID)

AF:

0.229

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.195

AC:

13266

AN:

67968

Other (OTH)

AF:

0.216

AC:

452

AN:

2096

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1294

2589

3883

5178

6472

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

330

660

990

1320

1650

<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:

0.201

Hom.:

10643

Bravo

AF:

0.228

Asia WGS

AF:

0.109

AC:

382

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.1

(source)

DANN

Benign

0.76

PhyloP100

-0.52

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