Genetic Variant ENST00000531511.1:n.409G>A (chr11-76654411-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 ENST00000531511.1(ENSG00000254810):n.409G>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 0.502 in 152,018 control chromosomes in the GnomAD database, including 19,444 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 0.50 ( 19430 hom., cov: 32)

Exomes 𝑓: 0.52 ( 14 hom. )

Consequence

ENSG00000254810
ENST00000531511.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.551

Publications

1 publications found

Variant links:

Genes affected

ENSG00000254810 (HGNC:):

ENSG00000254810 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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000254810	ENST00000531511.1 link	n.409G>A	non_coding_transcript_exon_variant	Exon 2 of 2	3
ENSG00000254810	ENST00000686694.2 link	n.493-554G>A	intron_variant	Intron 1 of 1
ENSG00000254810	ENST00000739657.1 link	n.454+2038G>A	intron_variant	Intron 1 of 1
ENSG00000254810	ENST00000739658.1 link	n.315-554G>A	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.502

AC:

76207

AN:

151810

Hom.:

19412

Cov.:

show subpopulations

Gnomad AFR

AF:

0.466

Gnomad AMI

AF:

0.569

Gnomad AMR

AF:

0.449

Gnomad ASJ

AF:

0.456

Gnomad EAS

AF:

0.544

Gnomad SAS

AF:

0.533

Gnomad FIN

AF:

0.511

Gnomad MID

AF:

0.421

Gnomad NFE

AF:

0.531

Gnomad OTH

AF:

0.479

GnomAD4 exome

AF:

0.522

AC:

AN:

Hom.:

Cov.:

AF XY:

0.517

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.667

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.750

AC:

AN:

South Asian (SAS)

AF:

0.750

AC:

AN:

European-Finnish (FIN)

AF:

0.583

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.442

AC:

AN:

Other (OTH)

AF:

0.583

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

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:

0.502

AC:

76262

AN:

151928

Hom.:

19430

Cov.:

AF XY:

0.499

AC XY:

37035

AN XY:

74228

show subpopulations

African (AFR)

AF:

0.466

AC:

19320

AN:

41420

American (AMR)

AF:

0.449

AC:

6859

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.456

AC:

1582

AN:

3472

East Asian (EAS)

AF:

0.544

AC:

2806

AN:

5158

South Asian (SAS)

AF:

0.535

AC:

2573

AN:

4812

European-Finnish (FIN)

AF:

0.511

AC:

5383

AN:

10536

Middle Eastern (MID)

AF:

0.422

AC:

124

AN:

294

European-Non Finnish (NFE)

AF:

0.531

AC:

36085

AN:

67930

Other (OTH)

AF:

0.480

AC:

1011

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1948

3896

5844

7792

9740

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

696

1392

2088

2784

3480

<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:

0.510

Hom.:

23710

Bravo

AF:

0.497

Asia WGS

AF:

0.550

AC:

1915

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.46

(source)

DANN

Benign

0.67

PhyloP100

-0.55

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