Genetic Variant ENST00000583462.1:n.38C>T (chr17-40014592-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 ENST00000583462.1(ENSG00000265799):n.38C>T 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 0.308 in 152,100 control chromosomes in the GnomAD database, including 8,405 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 0.31 ( 8400 hom., cov: 31)

Exomes 𝑓: 0.35 ( 5 hom. )

Consequence

ENSG00000265799
ENST00000583462.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.129

Publications

24 publications found

Variant links:

Genes affected

ENSG00000265799 (HGNC:58140):

ENSG00000265799 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=-0.8).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PSMD3-AS1	NR_198981.1 link	n.50C>T		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000265799	ENST00000583462.1 link	n.38C>T	non_coding_transcript_exon_variant	Exon 1 of 2	3
ENSG00000265799	ENST00000584649.1 link	n.114C>T	non_coding_transcript_exon_variant	Exon 1 of 3	4
ENSG00000265799	ENST00000801108.1 link	n.127C>T	non_coding_transcript_exon_variant	Exon 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.308

AC:

46763

AN:

151870

Hom.:

8409

Cov.:

show subpopulations

Gnomad AFR

AF:

0.115

Gnomad AMI

AF:

0.326

Gnomad AMR

AF:

0.400

Gnomad ASJ

AF:

0.417

Gnomad EAS

AF:

0.415

Gnomad SAS

AF:

0.464

Gnomad FIN

AF:

0.321

Gnomad MID

AF:

0.487

Gnomad NFE

AF:

0.375

Gnomad OTH

AF:

0.367

GnomAD4 exome

AF:

0.348

AC:

AN:

112

Hom.:

Cov.:

AF XY:

0.351

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.333

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.200

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.371

AC:

AN:

Other (OTH)

AF:

0.429

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.465

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:

0.308

AC:

46751

AN:

151988

Hom.:

8400

Cov.:

AF XY:

0.309

AC XY:

22933

AN XY:

74272

show subpopulations

African (AFR)

AF:

0.115

AC:

4787

AN:

41498

American (AMR)

AF:

0.399

AC:

6087

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.417

AC:

1445

AN:

3468

East Asian (EAS)

AF:

0.415

AC:

2130

AN:

5134

South Asian (SAS)

AF:

0.463

AC:

2230

AN:

4814

European-Finnish (FIN)

AF:

0.321

AC:

3393

AN:

10564

Middle Eastern (MID)

AF:

0.486

AC:

143

AN:

294

European-Non Finnish (NFE)

AF:

0.375

AC:

25469

AN:

67928

Other (OTH)

AF:

0.365

AC:

771

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1534

3068

4602

6136

7670

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

488

976

1464

1952

2440

<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:

0.312

Hom.:

5305

Bravo

AF:

0.308

Asia WGS

AF:

0.406

AC:

1417

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

3.3

(source)

DANN

Benign

0.84

PhyloP100

-0.13

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