Genetic Variant ENSG00000300614:n.260T>G (chr15-89358801-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000772988.1(ENSG00000300614):n.260T>G 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 0.527 in 152,212 control chromosomes in the GnomAD database, including 23,697 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 0.53 ( 23691 hom., cov: 33)

Exomes 𝑓: 0.36 ( 6 hom. )

Consequence

ENSG00000300614
ENST00000772988.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.473

Publications

15 publications found

Variant links:

Genes affected

ENSG00000300614 (HGNC:):

ENSG00000300614 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=-0.79).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903549	XR_007064750.1 link	n.-135T>G		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000300614	ENST00000772988.1 link	n.260T>G	non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000300614	ENST00000772990.1 link	n.233T>G	non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000279708	ENST00000624115.1 link	n.-40A>C	upstream_gene_variant		6
ENSG00000300614	ENST00000772989.1 link	n.-92T>G	upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.527

AC:

80150

AN:

152000

Hom.:

23648

Cov.:

show subpopulations

Gnomad AFR

AF:

0.806

Gnomad AMI

AF:

0.480

Gnomad AMR

AF:

0.428

Gnomad ASJ

AF:

0.370

Gnomad EAS

AF:

0.259

Gnomad SAS

AF:

0.483

Gnomad FIN

AF:

0.459

Gnomad MID

AF:

0.453

Gnomad NFE

AF:

0.424

Gnomad OTH

AF:

0.493

GnomAD4 exome

AF:

0.362

AC:

AN:

Hom.:

Cov.:

AF XY:

0.353

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.400

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.344

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.470

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.527

AC:

80238

AN:

152118

Hom.:

23691

Cov.:

AF XY:

0.528

AC XY:

39270

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.806

AC:

33466

AN:

41528

American (AMR)

AF:

0.427

AC:

6540

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.370

AC:

1284

AN:

3470

East Asian (EAS)

AF:

0.259

AC:

1331

AN:

5140

South Asian (SAS)

AF:

0.482

AC:

2323

AN:

4824

European-Finnish (FIN)

AF:

0.459

AC:

4849

AN:

10570

Middle Eastern (MID)

AF:

0.449

AC:

132

AN:

294

European-Non Finnish (NFE)

AF:

0.424

AC:

28850

AN:

67970

Other (OTH)

AF:

0.487

AC:

1026

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1784

3567

5351

7134

8918

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

676

1352

2028

2704

3380

<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:

0.427

Hom.:

28018

Bravo

AF:

0.538

Asia WGS

AF:

0.408

AC:

1417

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

7.1

(source)

DANN

Benign

0.18

PhyloP100

-0.47

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