Genetic Variant ENSG00000285040:n.1G>A (chr16-85985027-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 ENST00000822166.1(ENSG00000285040):n.1G>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 0.644 in 152,424 control chromosomes in the GnomAD database, including 32,059 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 0.64 ( 32009 hom., cov: 32)

Exomes 𝑓: 0.58 ( 50 hom. )

Consequence

ENSG00000285040
ENST00000822166.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.61

Publications

44 publications found

Variant links:

Genes affected

ENSG00000285040 (HGNC:):

ENSG00000285040 links:

ENSG00000269667 (HGNC:58164):

ENSG00000269667 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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903741	XR_007065161.1 link	n.271G>A		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000285040	ENST00000822166.1 link	n.1G>A	non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000285040	ENST00000645754.1 link	n.69+291G>A	intron_variant	Intron 1 of 2
ENSG00000269667	ENST00000599411.3 link	n.*143C>T	downstream_gene_variant		5

Frequencies

GnomAD3 genomes

AF:

0.645

AC:

97993

AN:

152032

Hom.:

31998

Cov.:

show subpopulations

Gnomad AFR

AF:

0.612

Gnomad AMI

AF:

0.780

Gnomad AMR

AF:

0.766

Gnomad ASJ

AF:

0.712

Gnomad EAS

AF:

0.870

Gnomad SAS

AF:

0.769

Gnomad FIN

AF:

0.539

Gnomad MID

AF:

0.772

Gnomad NFE

AF:

0.620

Gnomad OTH

AF:

0.690

GnomAD4 exome

AF:

0.584

AC:

160

AN:

274

Hom.:

AF XY:

0.514

AC XY:

AN XY:

148

show subpopulations

African (AFR)

AF:

0.250

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.750

AC:

AN:

East Asian (EAS)

AF:

0.808

AC:

AN:

South Asian (SAS)

AF:

1.00

AC:

AN:

European-Finnish (FIN)

AF:

0.278

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.579

AC:

117

AN:

202

Other (OTH)

AF:

0.583

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

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:

0.644

AC:

98041

AN:

152150

Hom.:

32009

Cov.:

AF XY:

0.647

AC XY:

48104

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.612

AC:

25392

AN:

41510

American (AMR)

AF:

0.767

AC:

11724

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.712

AC:

2471

AN:

3470

East Asian (EAS)

AF:

0.869

AC:

4502

AN:

5178

South Asian (SAS)

AF:

0.770

AC:

3709

AN:

4816

European-Finnish (FIN)

AF:

0.539

AC:

5691

AN:

10568

Middle Eastern (MID)

AF:

0.765

AC:

225

AN:

294

European-Non Finnish (NFE)

AF:

0.620

AC:

42173

AN:

68002

Other (OTH)

AF:

0.685

AC:

1443

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1781

3563

5344

7126

8907

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

792

1584

2376

3168

3960

<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:

0.635

Hom.:

105424

Bravo

AF:

0.663

Asia WGS

AF:

0.771

AC:

2678

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.5

(source)

DANN

Benign

0.74

PhyloP100

-1.6

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