Genetic Variant ENSG00000306949:n.451-44618G>A (chr11-38245666-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000822141.1(ENSG00000306949):n.451-44618G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0799 in 151,594 control chromosomes in the GnomAD database, including 1,567 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 0.080 ( 1567 hom., cov: 32)

Consequence

ENSG00000306949
ENST00000822141.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.925

Publications

0 publications found

Variant links:

Genes affected

ENSG00000306949 (HGNC:):

ENSG00000306949 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=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376634	XR_931202.2 link	n.555-44618G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306949	ENST00000822141.1 link	n.451-44618G>A		intron_variant	Intron 2 of 3
ENSG00000306949	ENST00000822142.1 link	n.455-44618G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.0797

AC:

12070

AN:

151476

Hom.:

1557

Cov.:

show subpopulations

Gnomad AFR

AF:

0.264

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0284

Gnomad ASJ

AF:

0.00896

Gnomad EAS

AF:

0.0236

Gnomad SAS

AF:

0.00786

Gnomad FIN

AF:

0.00472

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.00547

Gnomad OTH

AF:

0.0615

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

GnomAD4 genome

AF:

0.0799

AC:

12115

AN:

151594

Hom.:

1567

Cov.:

AF XY:

0.0773

AC XY:

5728

AN XY:

74104

show subpopulations

African (AFR)

AF:

0.264

AC:

10938

AN:

41412

American (AMR)

AF:

0.0283

AC:

430

AN:

15214

Ashkenazi Jewish (ASJ)

AF:

0.00896

AC:

AN:

3460

East Asian (EAS)

AF:

0.0234

AC:

121

AN:

5164

South Asian (SAS)

AF:

0.00829

AC:

AN:

4828

European-Finnish (FIN)

AF:

0.00472

AC:

AN:

10590

Middle Eastern (MID)

AF:

0.0204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00547

AC:

370

AN:

67616

Other (OTH)

AF:

0.0613

AC:

129

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

473

945

1418

1890

2363

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

114

228

342

456

570

<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:

0.0501

Hom.:

102

Bravo

AF:

0.0898

Asia WGS

AF:

0.0330

AC:

116

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.32

(source)

DANN

Benign

0.18

PhyloP100

-0.93

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