Genetic Variant ENSG00000231204:n.120+64926T>C (chr2-21286220-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000435237.1(ENSG00000231204):n.120+64926T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 152,064 control chromosomes in the GnomAD database, including 5,940 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 0.27 ( 5940 hom., cov: 31)

Consequence

ENSG00000231204
ENST00000435237.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.73

Publications

4 publications found

Variant links:

Genes affected

ENSG00000231204 (HGNC:):

ENSG00000231204 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=-0.96).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.314 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
ENSG00000231204	ENST00000435237.1 link	n.120+64926T>C		intron_variant	Intron 1 of 5	3

Frequencies

GnomAD3 genomes

AF:

0.271

AC:

41195

AN:

151946

Hom.:

5927

Cov.:

show subpopulations

Gnomad AFR

AF:

0.212

Gnomad AMI

AF:

0.366

Gnomad AMR

AF:

0.213

Gnomad ASJ

AF:

0.207

Gnomad EAS

AF:

0.170

Gnomad SAS

AF:

0.286

Gnomad FIN

AF:

0.353

Gnomad MID

AF:

0.237

Gnomad NFE

AF:

0.318

Gnomad OTH

AF:

0.223

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

GnomAD4 genome

AF:

0.271

AC:

41242

AN:

152064

Hom.:

5940

Cov.:

AF XY:

0.273

AC XY:

20288

AN XY:

74340

show subpopulations

African (AFR)

AF:

0.213

AC:

8811

AN:

41462

American (AMR)

AF:

0.213

AC:

3248

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.207

AC:

719

AN:

3466

East Asian (EAS)

AF:

0.170

AC:

879

AN:

5166

South Asian (SAS)

AF:

0.287

AC:

1380

AN:

4814

European-Finnish (FIN)

AF:

0.353

AC:

3738

AN:

10584

Middle Eastern (MID)

AF:

0.228

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.318

AC:

21593

AN:

67974

Other (OTH)

AF:

0.224

AC:

474

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1521

3041

4562

6082

7603

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

430

860

1290

1720

2150

<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:

0.285

Hom.:

795

Bravo

AF:

0.254

Asia WGS

AF:

0.222

AC:

779

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.080

(source)

DANN

Benign

0.42

PhyloP100

-2.7

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