Genetic Variant ENST00000794040.1:n.277-7121G>A (chr10-120329400-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 ENST00000794040.1(ENSG00000303377):n.277-7121G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 151,178 control chromosomes in the GnomAD database, including 4,299 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 0.23 ( 4299 hom., cov: 31)

Consequence

ENSG00000303377
ENST00000794040.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.306

Publications

2 publications found

Variant links:

Genes affected

ENSG00000303377 (HGNC:):

ENSG00000303377 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=-1.0).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378515	XR_001747606.1 link	n.994-7121G>A		intron_variant	Intron 7 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303377	ENST00000794040.1 link	n.277-7121G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.229

AC:

34544

AN:

151062

Hom.:

4295

Cov.:

show subpopulations

Gnomad AFR

AF:

0.187

Gnomad AMI

AF:

0.364

Gnomad AMR

AF:

0.165

Gnomad ASJ

AF:

0.253

Gnomad EAS

AF:

0.253

Gnomad SAS

AF:

0.336

Gnomad FIN

AF:

0.406

Gnomad MID

AF:

0.0892

Gnomad NFE

AF:

0.229

Gnomad OTH

AF:

0.222

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

GnomAD4 genome

AF:

0.229

AC:

34555

AN:

151178

Hom.:

4299

Cov.:

AF XY:

0.237

AC XY:

17551

AN XY:

73926

show subpopulations

African (AFR)

AF:

0.187

AC:

7591

AN:

40640

American (AMR)

AF:

0.165

AC:

2520

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.253

AC:

878

AN:

3466

East Asian (EAS)

AF:

0.253

AC:

1306

AN:

5160

South Asian (SAS)

AF:

0.335

AC:

1615

AN:

4816

European-Finnish (FIN)

AF:

0.406

AC:

4288

AN:

10566

Middle Eastern (MID)

AF:

0.0822

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.229

AC:

15538

AN:

67960

Other (OTH)

AF:

0.221

AC:

464

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1345

2690

4035

5380

6725

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.230

Hom.:

3135

Bravo

AF:

0.205

Asia WGS

AF:

0.291

AC:

1009

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

2.1

(source)

DANN

Benign

0.34

PhyloP100

0.31

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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ENST00000794040.1:n.277-7121G>A

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