dbSNP rs346054: ENSG00000283525:n.1512G>C (chr19-43700317-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000636801.1(ENSG00000283525):n.1512G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 152,154 control chromosomes in the GnomAD database, including 17,944 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 0.47 ( 17928 hom., cov: 33)

Exomes 𝑓: 0.59 ( 16 hom. )

Consequence

ENSG00000283525
ENST00000636801.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.12

Publications

2 publications found

Variant links:

Genes affected

ENSG00000283525 (HGNC:):

ENSG00000283525 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 (NFE) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372412	NR_172891.1 link	n.2178G>C		non_coding_transcript_exon_variant	Exon 7 of 7

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000283525	ENST00000636801.1 link	n.1512G>C	non_coding_transcript_exon_variant	Exon 6 of 6	6
ENSG00000290609	ENST00000637093.1 link	n.1352G>C	non_coding_transcript_exon_variant	Exon 5 of 5	5
ENSG00000290609	ENST00000737707.1 link	n.1083G>C	non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000290609	ENST00000737708.1 link	n.406-13G>C	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.471

AC:

71583

AN:

151944

Hom.:

17921

Cov.:

show subpopulations

Gnomad AFR

AF:

0.289

Gnomad AMI

AF:

0.628

Gnomad AMR

AF:

0.521

Gnomad ASJ

AF:

0.456

Gnomad EAS

AF:

0.472

Gnomad SAS

AF:

0.517

Gnomad FIN

AF:

0.566

Gnomad MID

AF:

0.471

Gnomad NFE

AF:

0.550

Gnomad OTH

AF:

0.492

GnomAD4 exome

AF:

0.589

AC:

AN:

Hom.:

Cov.:

AF XY:

0.553

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.750

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.571

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.471

AC:

71623

AN:

152064

Hom.:

17928

Cov.:

AF XY:

0.473

AC XY:

35140

AN XY:

74312

show subpopulations

African (AFR)

AF:

0.290

AC:

12021

AN:

41496

American (AMR)

AF:

0.521

AC:

7962

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.456

AC:

1580

AN:

3468

East Asian (EAS)

AF:

0.473

AC:

2431

AN:

5140

South Asian (SAS)

AF:

0.516

AC:

2489

AN:

4822

European-Finnish (FIN)

AF:

0.566

AC:

5990

AN:

10582

Middle Eastern (MID)

AF:

0.473

AC:

139

AN:

294

European-Non Finnish (NFE)

AF:

0.550

AC:

37406

AN:

67966

Other (OTH)

AF:

0.492

AC:

1035

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1904

3809

5713

7618

9522

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

654

1308

1962

2616

3270

<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:

0.504

Hom.:

2499

Bravo

AF:

0.457

Asia WGS

AF:

0.495

AC:

1723

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

5.8

(source)

DANN

Benign

0.59

PhyloP100

1.1

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over