Genetic Variant ENSG00000301575:n.368C>T (chr2-236684247-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 ENST00000779927.1(ENSG00000301575):n.368C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0654 in 152,228 control chromosomes in the GnomAD database, including 397 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 0.065 ( 397 hom., cov: 32)

Consequence

ENSG00000301575
ENST00000779927.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0720

Publications

1 publications found

Variant links:

Genes affected

ENSG00000301575 (HGNC:):

ENSG00000301575 links:

Genome browser will be placed here

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 = 0.0717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000301575	ENST00000779927.1 link	n.368C>T	non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000301575	ENST00000779928.1 link	n.179C>T	non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000301575	ENST00000779929.1 link	n.295C>T	non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.0654

AC:

9948

AN:

152110

Hom.:

397

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0515

Gnomad AMI

AF:

0.0746

Gnomad AMR

AF:

0.0430

Gnomad ASJ

AF:

0.102

Gnomad EAS

AF:

0.00290

Gnomad SAS

AF:

0.0276

Gnomad FIN

AF:

0.138

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.0734

Gnomad OTH

AF:

0.0555

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

GnomAD4 genome

AF:

0.0654

AC:

9950

AN:

152228

Hom.:

397

Cov.:

AF XY:

0.0672

AC XY:

5001

AN XY:

74428

show subpopulations

African (AFR)

AF:

0.0514

AC:

2135

AN:

41540

American (AMR)

AF:

0.0428

AC:

655

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.102

AC:

353

AN:

3470

East Asian (EAS)

AF:

0.00290

AC:

AN:

5168

South Asian (SAS)

AF:

0.0280

AC:

135

AN:

4820

European-Finnish (FIN)

AF:

0.138

AC:

1461

AN:

10602

Middle Eastern (MID)

AF:

0.0612

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0734

AC:

4994

AN:

68018

Other (OTH)

AF:

0.0549

AC:

116

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

496

992

1488

1984

2480

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

116

232

348

464

580

<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:

0.0745

Hom.:

Bravo

AF:

0.0583

Asia WGS

AF:

0.0150

AC:

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

2.5

(source)

DANN

Benign

0.83

PhyloP100

-0.072

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