dbSNP rs346923: ENSG00000287999:n.102+5510C>T (chr4-52545963-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 ENST00000660768.1(ENSG00000287999):n.102+5510C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,066 control chromosomes in the GnomAD database, including 4,436 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 0.20 ( 4436 hom., cov: 32)

Consequence

ENSG00000287999
ENST00000660768.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.03

Publications

6 publications found

Variant links:

Genes affected

ENSG00000287999 (HGNC:):

ENSG00000287999 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=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000287999	ENST00000660768.1 link	n.102+5510C>T	intron_variant	Intron 1 of 2
ENSG00000287999	ENST00000757447.1 link	n.140+5510C>T	intron_variant	Intron 1 of 4
ENSG00000287999	ENST00000757448.1 link	n.98+5510C>T	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.201

AC:

30548

AN:

151948

Hom.:

4413

Cov.:

show subpopulations

Gnomad AFR

AF:

0.415

Gnomad AMI

AF:

0.111

Gnomad AMR

AF:

0.135

Gnomad ASJ

AF:

0.182

Gnomad EAS

AF:

0.206

Gnomad SAS

AF:

0.133

Gnomad FIN

AF:

0.0799

Gnomad MID

AF:

0.168

Gnomad NFE

AF:

0.111

Gnomad OTH

AF:

0.192

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

GnomAD4 genome

AF:

0.201

AC:

30626

AN:

152066

Hom.:

4436

Cov.:

AF XY:

0.197

AC XY:

14635

AN XY:

74326

show subpopulations

African (AFR)

AF:

0.416

AC:

17233

AN:

41444

American (AMR)

AF:

0.135

AC:

2065

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.182

AC:

629

AN:

3462

East Asian (EAS)

AF:

0.206

AC:

1062

AN:

5166

South Asian (SAS)

AF:

0.133

AC:

640

AN:

4812

European-Finnish (FIN)

AF:

0.0799

AC:

845

AN:

10572

Middle Eastern (MID)

AF:

0.180

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.112

AC:

7584

AN:

68018

Other (OTH)

AF:

0.196

AC:

414

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1101

2201

3302

4402

5503

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

300

600

900

1200

1500

<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:

0.149

Hom.:

5678

Bravo

AF:

0.216

Asia WGS

AF:

0.191

AC:

665

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

8.7

(source)

DANN

Benign

0.75

PhyloP100

1.0

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