Genetic Variant ENSG00000304972:n.153-4414G>T (chr4-181301574-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000807466.1(ENSG00000304972):n.153-4414G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,004 control chromosomes in the GnomAD database, including 1,306 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 0.13 ( 1306 hom., cov: 32)

Consequence

ENSG00000304972
ENST00000807466.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.67

Publications

2 publications found

Variant links:

Genes affected

ENSG00000304972 (HGNC:):

ENSG00000304972 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 = 0.158 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
ENSG00000304972	ENST00000807466.1 link	n.153-4414G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.125

AC:

19015

AN:

151886

Hom.:

1307

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0958

Gnomad AMI

AF:

0.0504

Gnomad AMR

AF:

0.102

Gnomad ASJ

AF:

0.106

Gnomad EAS

AF:

0.0390

Gnomad SAS

AF:

0.0455

Gnomad FIN

AF:

0.138

Gnomad MID

AF:

0.105

Gnomad NFE

AF:

0.160

Gnomad OTH

AF:

0.132

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

GnomAD4 genome

AF:

0.125

AC:

19018

AN:

152004

Hom.:

1306

Cov.:

AF XY:

0.122

AC XY:

9026

AN XY:

74286

show subpopulations

African (AFR)

AF:

0.0956

AC:

3967

AN:

41486

American (AMR)

AF:

0.102

AC:

1555

AN:

15242

Ashkenazi Jewish (ASJ)

AF:

0.106

AC:

369

AN:

3468

East Asian (EAS)

AF:

0.0391

AC:

201

AN:

5144

South Asian (SAS)

AF:

0.0455

AC:

219

AN:

4814

European-Finnish (FIN)

AF:

0.138

AC:

1464

AN:

10588

Middle Eastern (MID)

AF:

0.110

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.160

AC:

10890

AN:

67956

Other (OTH)

AF:

0.131

AC:

275

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

838

1676

2513

3351

4189

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

210

420

630

840

1050

<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:

0.148

Hom.:

6450

Bravo

AF:

0.123

Asia WGS

AF:

0.0460

AC:

160

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

0.10

(source)

DANN

Benign

0.54

PhyloP100

-1.7

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