Genetic Variant ENSG00000263655:n.685A>C (chr18-73914271-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000753906.1(ENSG00000263655):n.685A>C 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 0.328 in 151,960 control chromosomes in the GnomAD database, including 8,695 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 0.33 ( 8695 hom., cov: 31)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

ENSG00000263655
ENST00000753906.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.644

Publications

4 publications found

Variant links:

Genes affected

ENSG00000263655 (HGNC:):

ENSG00000263655 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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.612 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
ENSG00000263655	ENST00000753906.1 link	n.685A>C	non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000263655	ENST00000753907.1 link	n.696A>C	non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000263655	ENST00000581541.1 link	n.*134A>C	downstream_gene_variant		3

Frequencies

GnomAD3 genomes

AF:

0.328

AC:

49878

AN:

151842

Hom.:

8689

Cov.:

show subpopulations

Gnomad AFR

AF:

0.343

Gnomad AMI

AF:

0.275

Gnomad AMR

AF:

0.222

Gnomad ASJ

AF:

0.312

Gnomad EAS

AF:

0.632

Gnomad SAS

AF:

0.475

Gnomad FIN

AF:

0.346

Gnomad MID

AF:

0.301

Gnomad NFE

AF:

0.309

Gnomad OTH

AF:

0.329

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

Hom.:

AF XY:

0.00

AC XY:

AN XY:

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:

0.00

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.328

AC:

49912

AN:

151960

Hom.:

8695

Cov.:

AF XY:

0.332

AC XY:

24671

AN XY:

74270

show subpopulations

African (AFR)

AF:

0.343

AC:

14232

AN:

41440

American (AMR)

AF:

0.222

AC:

3380

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.312

AC:

1081

AN:

3470

East Asian (EAS)

AF:

0.630

AC:

3253

AN:

5160

South Asian (SAS)

AF:

0.477

AC:

2294

AN:

4814

European-Finnish (FIN)

AF:

0.346

AC:

3652

AN:

10552

Middle Eastern (MID)

AF:

0.297

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.309

AC:

20987

AN:

67954

Other (OTH)

AF:

0.330

AC:

696

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1679

3359

5038

6718

8397

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

502

1004

1506

2008

2510

<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.:

4880

Bravo

AF:

0.316

Asia WGS

AF:

0.541

AC:

1880

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

(source)

DANN

Benign

0.52

PhyloP100

0.64

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over