Genetic Variant ENST00000740305.1:n.238G>A (chr7-76301483-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 ENST00000740305.1(ENSG00000296557):n.238G>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 0.156 in 151,592 control chromosomes in the GnomAD database, including 2,048 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 0.16 ( 2048 hom., cov: 32)

Consequence

ENSG00000296557
ENST00000740305.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.901

Publications

11 publications found

Variant links:

Genes affected

ENSG00000296557 (HGNC:):

ENSG00000296557 links:

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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=-0.95).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296557	ENST00000740305.1 link	n.238G>A		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000296557	ENST00000740306.1 link	n.196-1119G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.156

AC:

23576

AN:

151484

Hom.:

2049

Cov.:

show subpopulations

Gnomad AFR

AF:

0.101

Gnomad AMI

AF:

0.0165

Gnomad AMR

AF:

0.184

Gnomad ASJ

AF:

0.0987

Gnomad EAS

AF:

0.183

Gnomad SAS

AF:

0.121

Gnomad FIN

AF:

0.289

Gnomad MID

AF:

0.0732

Gnomad NFE

AF:

0.168

Gnomad OTH

AF:

0.139

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.156

AC:

23574

AN:

151592

Hom.:

2048

Cov.:

AF XY:

0.159

AC XY:

11758

AN XY:

73994

show subpopulations

African (AFR)

AF:

0.101

AC:

4180

AN:

41398

American (AMR)

AF:

0.184

AC:

2794

AN:

15192

Ashkenazi Jewish (ASJ)

AF:

0.0987

AC:

342

AN:

3466

East Asian (EAS)

AF:

0.183

AC:

943

AN:

5154

South Asian (SAS)

AF:

0.119

AC:

573

AN:

4808

European-Finnish (FIN)

AF:

0.289

AC:

2989

AN:

10352

Middle Eastern (MID)

AF:

0.0719

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.168

AC:

11428

AN:

67922

Other (OTH)

AF:

0.138

AC:

289

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

965

1929

2894

3858

4823

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

260

520

780

1040

1300

<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:

0.163

Hom.:

256

Bravo

AF:

0.148

Asia WGS

AF:

0.174

AC:

605

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

4.9

(source)

DANN

Benign

0.48

PhyloP100

-0.90

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