Genetic Variant ENSG00000304642:n.685+22109C>T (chr2-136149559-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 ENST00000805101.1(ENSG00000304642):n.685+22109C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,102 control chromosomes in the GnomAD database, including 1,453 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 0.12 ( 1453 hom., cov: 32)

Consequence

ENSG00000304642
ENST00000805101.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0650

Publications

7 publications found

Variant links:

Genes affected

ENSG00000304642 (HGNC:):

ENSG00000304642 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 = 0.287 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
ENSG00000304642	ENST00000805101.1 link	n.685+22109C>T		intron_variant	Intron 1 of 1
ENSG00000304642	ENST00000805102.1 link	n.142-6764C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.118

AC:

17934

AN:

151984

Hom.:

1457

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0262

Gnomad AMI

AF:

0.238

Gnomad AMR

AF:

0.175

Gnomad ASJ

AF:

0.251

Gnomad EAS

AF:

0.300

Gnomad SAS

AF:

0.208

Gnomad FIN

AF:

0.163

Gnomad MID

AF:

0.325

Gnomad NFE

AF:

0.123

Gnomad OTH

AF:

0.159

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

GnomAD4 genome

AF:

0.118

AC:

17921

AN:

152102

Hom.:

1453

Cov.:

AF XY:

0.124

AC XY:

9186

AN XY:

74314

show subpopulations

African (AFR)

AF:

0.0262

AC:

1087

AN:

41528

American (AMR)

AF:

0.175

AC:

2672

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.251

AC:

870

AN:

3470

East Asian (EAS)

AF:

0.299

AC:

1539

AN:

5140

South Asian (SAS)

AF:

0.209

AC:

1007

AN:

4818

European-Finnish (FIN)

AF:

0.163

AC:

1720

AN:

10574

Middle Eastern (MID)

AF:

0.312

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.123

AC:

8384

AN:

67978

Other (OTH)

AF:

0.158

AC:

334

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

794

1587

2381

3174

3968

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

204

408

612

816

1020

<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:

0.116

Hom.:

692

Bravo

AF:

0.115

Asia WGS

AF:

0.236

AC:

818

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

1.4

(source)

DANN

Benign

0.73

PhyloP100

0.065

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