Genetic Variant ENSG00000304890:n.249+1698T>C (chr12-27330924-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000806970.1(ENSG00000304890):n.249+1698T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0695 in 152,248 control chromosomes in the GnomAD database, including 481 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 0.069 ( 481 hom., cov: 31)

Consequence

ENSG00000304890
ENST00000806970.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.512

Publications

4 publications found

Variant links:

Genes affected

ENSG00000304890 (HGNC:):

ENSG00000304890 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=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902906	XR_007063255.1 link	n.176+1698T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000304890	ENST00000806970.1 link	n.249+1698T>C	intron_variant	Intron 1 of 1
ENSG00000304890	ENST00000806971.1 link	n.233+1698T>C	intron_variant	Intron 1 of 2
ENSG00000304890	ENST00000806972.1 link	n.193+1698T>C	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.0695

AC:

10579

AN:

152130

Hom.:

481

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0166

Gnomad AMI

AF:

0.156

Gnomad AMR

AF:

0.0445

Gnomad ASJ

AF:

0.0766

Gnomad EAS

AF:

0.0406

Gnomad SAS

AF:

0.0497

Gnomad FIN

AF:

0.106

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.104

Gnomad OTH

AF:

0.0542

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

GnomAD4 genome

AF:

0.0695

AC:

10576

AN:

152248

Hom.:

481

Cov.:

AF XY:

0.0686

AC XY:

5108

AN XY:

74432

show subpopulations

African (AFR)

AF:

0.0165

AC:

687

AN:

41554

American (AMR)

AF:

0.0444

AC:

679

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0766

AC:

266

AN:

3472

East Asian (EAS)

AF:

0.0407

AC:

211

AN:

5180

South Asian (SAS)

AF:

0.0498

AC:

240

AN:

4824

European-Finnish (FIN)

AF:

0.106

AC:

1121

AN:

10608

Middle Eastern (MID)

AF:

0.0340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.104

AC:

7106

AN:

68012

Other (OTH)

AF:

0.0541

AC:

114

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

503

1006

1509

2012

2515

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

124

248

372

496

620

<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:

0.0962

Hom.:

111

Bravo

AF:

0.0610

Asia WGS

AF:

0.0430

AC:

151

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

2.2

(source)

DANN

Benign

0.64

PhyloP100

-0.51

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