Genetic Variant ENSG00000288731:n.260G>A (chr19-35433855-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 ENST00000716259.1(ENSG00000288731):n.260G>A 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 0.272 in 152,156 control chromosomes in the GnomAD database, including 5,881 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 0.27 ( 5877 hom., cov: 32)

Exomes 𝑓: 0.48 ( 4 hom. )

Consequence

ENSG00000288731
ENST00000716259.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.53

Publications

4 publications found

Variant links:

Genes affected

ENSG00000288731 (HGNC:):

ENSG00000288731 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=-0.96).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927522	NR_187751.1 link	n.335-17G>A		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000288731	ENST00000716259.1 link	n.260G>A	non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000288731	ENST00000786314.1 link	n.259G>A	non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000288731	ENST00000786318.1 link	n.814G>A	non_coding_transcript_exon_variant	Exon 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.272

AC:

41358

AN:

151994

Hom.:

5867

Cov.:

show subpopulations

Gnomad AFR

AF:

0.204

Gnomad AMI

AF:

0.425

Gnomad AMR

AF:

0.323

Gnomad ASJ

AF:

0.297

Gnomad EAS

AF:

0.356

Gnomad SAS

AF:

0.324

Gnomad FIN

AF:

0.310

Gnomad MID

AF:

0.291

Gnomad NFE

AF:

0.283

Gnomad OTH

AF:

0.274

GnomAD4 exome

AF:

0.477

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.475

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.417

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.272

AC:

41412

AN:

152112

Hom.:

5877

Cov.:

AF XY:

0.275

AC XY:

20444

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.205

AC:

8493

AN:

41516

American (AMR)

AF:

0.323

AC:

4943

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.297

AC:

1030

AN:

3470

East Asian (EAS)

AF:

0.356

AC:

1837

AN:

5160

South Asian (SAS)

AF:

0.324

AC:

1562

AN:

4824

European-Finnish (FIN)

AF:

0.310

AC:

3273

AN:

10558

Middle Eastern (MID)

AF:

0.286

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.283

AC:

19223

AN:

67982

Other (OTH)

AF:

0.274

AC:

579

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1565

3130

4695

6260

7825

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

436

872

1308

1744

2180

<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:

0.267

Hom.:

3886

Bravo

AF:

0.269

Asia WGS

AF:

0.387

AC:

1347

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.19

(source)

DANN

Benign

0.56

PhyloP100

-1.5

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