Genetic Variant ENSG00000310371:n.102+3865G>C (chr13-26727717-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 ENST00000849353.1(ENSG00000310371):n.102+3865G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 150,996 control chromosomes in the GnomAD database, including 17,082 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 0.47 ( 17082 hom., cov: 32)

Consequence

ENSG00000310371
ENST00000849353.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.223

Publications

1 publications found

Variant links:

Genes affected

ENSG00000310371 (HGNC:):

ENSG00000310371 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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.596 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
ENSG00000310371	ENST00000849353.1 link	n.102+3865G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.472

AC:

71143

AN:

150880

Hom.:

17065

Cov.:

show subpopulations

Gnomad AFR

AF:

0.360

Gnomad AMI

AF:

0.480

Gnomad AMR

AF:

0.494

Gnomad ASJ

AF:

0.614

Gnomad EAS

AF:

0.614

Gnomad SAS

AF:

0.529

Gnomad FIN

AF:

0.411

Gnomad MID

AF:

0.620

Gnomad NFE

AF:

0.519

Gnomad OTH

AF:

0.509

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

GnomAD4 genome

AF:

0.471

AC:

71194

AN:

150996

Hom.:

17082

Cov.:

AF XY:

0.469

AC XY:

34597

AN XY:

73696

show subpopulations

African (AFR)

AF:

0.360

AC:

14797

AN:

41090

American (AMR)

AF:

0.494

AC:

7519

AN:

15208

Ashkenazi Jewish (ASJ)

AF:

0.614

AC:

2126

AN:

3462

East Asian (EAS)

AF:

0.614

AC:

3167

AN:

5156

South Asian (SAS)

AF:

0.530

AC:

2542

AN:

4796

European-Finnish (FIN)

AF:

0.411

AC:

4217

AN:

10252

Middle Eastern (MID)

AF:

0.612

AC:

180

AN:

294

European-Non Finnish (NFE)

AF:

0.519

AC:

35131

AN:

67722

Other (OTH)

AF:

0.512

AC:

1077

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1950

3899

5849

7798

9748

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

650

1300

1950

2600

3250

<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:

0.318

Hom.:

762

Bravo

AF:

0.469

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.68

(source)

DANN

Benign

0.60

PhyloP100

-0.22

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