Genetic Variant ENST00000776174.1:n.892G>C (chr4-119488539-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000776174.1(ENSG00000291203):n.892G>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 0.266 in 151,902 control chromosomes in the GnomAD database, including 5,471 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 0.27 ( 5469 hom., cov: 32)

Exomes 𝑓: 0.30 ( 2 hom. )

Consequence

ENSG00000291203
ENST00000776174.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.998

Publications

10 publications found

Variant links:

Genes affected

ENSG00000291203 (HGNC:):

ENSG00000291203 links:

SEPTIN7P14 (HGNC:44219): (septin 7 pseudogene 14)

SEPTIN7P14 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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SEPTIN7P14	NR_037630.1 link	n.728-4794G>C		intron_variant	Intron 5 of 8

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000291203	ENST00000776174.1 link	n.892G>C	non_coding_transcript_exon_variant	Exon 6 of 9
ENSG00000291203	ENST00000502760.2 link	n.772-4794G>C	intron_variant	Intron 6 of 9	3
ENSG00000291203	ENST00000508519.6 link	n.663-106G>C	intron_variant	Intron 5 of 10	3

Frequencies

GnomAD3 genomes

AF:

0.266

AC:

40308

AN:

151732

Hom.:

5464

Cov.:

show subpopulations

Gnomad AFR

AF:

0.227

Gnomad AMI

AF:

0.280

Gnomad AMR

AF:

0.264

Gnomad ASJ

AF:

0.190

Gnomad EAS

AF:

0.382

Gnomad SAS

AF:

0.177

Gnomad FIN

AF:

0.254

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.293

Gnomad OTH

AF:

0.280

GnomAD4 exome

AF:

0.300

AC:

AN:

Hom.:

AF XY:

0.206

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.286

AC:

AN:

Other (OTH)

AF:

0.750

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.530

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.266

AC:

40343

AN:

151852

Hom.:

5469

Cov.:

AF XY:

0.264

AC XY:

19565

AN XY:

74216

show subpopulations

African (AFR)

AF:

0.227

AC:

9405

AN:

41460

American (AMR)

AF:

0.264

AC:

4020

AN:

15226

Ashkenazi Jewish (ASJ)

AF:

0.190

AC:

658

AN:

3468

East Asian (EAS)

AF:

0.383

AC:

1960

AN:

5118

South Asian (SAS)

AF:

0.176

AC:

850

AN:

4820

European-Finnish (FIN)

AF:

0.254

AC:

2681

AN:

10572

Middle Eastern (MID)

AF:

0.207

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.293

AC:

19867

AN:

67876

Other (OTH)

AF:

0.278

AC:

587

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1508

3016

4524

6032

7540

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

420

840

1260

1680

2100

<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:

0.268

Hom.:

719

Bravo

AF:

0.271

Asia WGS

AF:

0.251

AC:

871

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.23

(source)

DANN

Benign

0.67

PhyloP100

-1.0

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