Genetic Variant ENSG00000249041:n.417-1299A>C (chr4-154756163-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000515071.1(ENSG00000249041):n.417-1299A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 151,972 control chromosomes in the GnomAD database, including 1,714 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 0.15 ( 1714 hom., cov: 31)

Consequence

ENSG00000249041
ENST00000515071.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0650

Publications

7 publications found

Variant links:

Genes affected

ENSG00000249041 (HGNC:):

ENSG00000249041 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=-0.74).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377500	NR_188451.1 link	n.417-1299A>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249041	ENST00000515071.1 link	n.417-1299A>C		intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes

AF:

0.145

AC:

22082

AN:

151856

Hom.:

1706

Cov.:

show subpopulations

Gnomad AFR

AF:

0.177

Gnomad AMI

AF:

0.0175

Gnomad AMR

AF:

0.0884

Gnomad ASJ

AF:

0.101

Gnomad EAS

AF:

0.219

Gnomad SAS

AF:

0.175

Gnomad FIN

AF:

0.200

Gnomad MID

AF:

0.140

Gnomad NFE

AF:

0.127

Gnomad OTH

AF:

0.140

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

GnomAD4 genome

AF:

0.145

AC:

22104

AN:

151972

Hom.:

1714

Cov.:

AF XY:

0.148

AC XY:

10981

AN XY:

74274

show subpopulations

African (AFR)

AF:

0.177

AC:

7339

AN:

41440

American (AMR)

AF:

0.0883

AC:

1347

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.101

AC:

352

AN:

3472

East Asian (EAS)

AF:

0.219

AC:

1130

AN:

5156

South Asian (SAS)

AF:

0.174

AC:

838

AN:

4806

European-Finnish (FIN)

AF:

0.200

AC:

2112

AN:

10558

Middle Eastern (MID)

AF:

0.143

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.127

AC:

8637

AN:

67966

Other (OTH)

AF:

0.138

AC:

291

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

938

1876

2813

3751

4689

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

250

500

750

1000

1250

<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:

0.127

Hom.:

2078

Bravo

AF:

0.139

Asia WGS

AF:

0.170

AC:

592

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

7.8

(source)

DANN

Benign

0.92

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