Genetic Variant ENST00000727371.1:n.307-13053T>C (chr1-157265756-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 ENST00000727371.1(ENSG00000295014):n.307-13053T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0371 in 152,208 control chromosomes in the GnomAD database, including 204 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 0.037 ( 204 hom., cov: 32)

Consequence

ENSG00000295014
ENST00000727371.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.120

Publications

1 publications found

Variant links:

Genes affected

ENSG00000295014 (HGNC:):

ENSG00000295014 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=-1.02).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.094 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371456	XR_922183.3 link	n.213-13053T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000295014	ENST00000727371.1 link	n.307-13053T>C	intron_variant	Intron 1 of 3
ENSG00000295014	ENST00000727372.1 link	n.277-13053T>C	intron_variant	Intron 1 of 3
ENSG00000295014	ENST00000727373.1 link	n.213-13053T>C	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0369

AC:

5619

AN:

152090

Hom.:

200

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0471

Gnomad AMI

AF:

0.110

Gnomad AMR

AF:

0.0979

Gnomad ASJ

AF:

0.00317

Gnomad EAS

AF:

0.0798

Gnomad SAS

AF:

0.0501

Gnomad FIN

AF:

0.0106

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0181

Gnomad OTH

AF:

0.0302

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

GnomAD4 genome

AF:

0.0371

AC:

5646

AN:

152208

Hom.:

204

Cov.:

AF XY:

0.0380

AC XY:

2825

AN XY:

74406

show subpopulations

African (AFR)

AF:

0.0475

AC:

1972

AN:

41528

American (AMR)

AF:

0.0982

AC:

1499

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.00317

AC:

AN:

3468

East Asian (EAS)

AF:

0.0798

AC:

413

AN:

5178

South Asian (SAS)

AF:

0.0498

AC:

240

AN:

4824

European-Finnish (FIN)

AF:

0.0106

AC:

112

AN:

10614

Middle Eastern (MID)

AF:

0.00680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0181

AC:

1231

AN:

68014

Other (OTH)

AF:

0.0313

AC:

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.442

Heterozygous variant carriers

251

501

752

1002

1253

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

124

186

248

310

<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:

0.0296

Hom.:

Bravo

AF:

0.0456

Asia WGS

AF:

0.0980

AC:

341

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.87

(source)

DANN

Benign

0.33

PhyloP100

-0.12

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