Genetic Variant ENSG00000248373:n.*82A>G (chr4-105120082-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000506386.1(ENSG00000248373):n.*82A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,210 control chromosomes in the GnomAD database, including 1,459 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 0.10 ( 1459 hom., cov: 33)

Exomes 𝑓: 0.083 ( 0 hom. )

Consequence

ENSG00000248373
ENST00000506386.1 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.37

Variant links:

Genes affected

ENSG00000248373 (HGNC:):

ENSG00000248373 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.253 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
ENSG00000248373	ENST00000506386.1 link	n.*82A>G		downstream_gene_variant		3
ENSG00000248373	ENST00000671069.1 link	n.*82A>G		downstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.100

AC:

15236

AN:

152080

Hom.:

1455

Cov.:

show subpopulations

Gnomad AFR

AF:

0.257

Gnomad AMI

AF:

0.101

Gnomad AMR

AF:

0.0452

Gnomad ASJ

AF:

0.109

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0377

Gnomad FIN

AF:

0.0436

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.0384

Gnomad OTH

AF:

0.0783

GnomAD4 exome

AF:

0.0833

AC:

AN:

Hom.:

AF XY:

0.00

AC XY:

AN XY:

show subpopulations

Gnomad4 NFE exome

AF:

0.0833

GnomAD4 genome

AF:

0.100

AC:

15256

AN:

152198

Hom.:

1459

Cov.:

AF XY:

0.0989

AC XY:

7358

AN XY:

74428

show subpopulations

Gnomad4 AFR

AF:

0.257

Gnomad4 AMR

AF:

0.0452

Gnomad4 ASJ

AF:

0.109

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0377

Gnomad4 FIN

AF:

0.0436

Gnomad4 NFE

AF:

0.0384

Gnomad4 OTH

AF:

0.0775

Alfa

AF:

0.0631

Hom.:

133

Bravo

AF:

0.108

Asia WGS

AF:

0.0270

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.24

DANN

Benign

0.56

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over