Genetic Variant ENST00000848457.1:n.204+3531C>T (chr6-98479487-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000848457.1(ENSG00000310228):n.204+3531C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0491 in 151,950 control chromosomes in the GnomAD database, including 229 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 0.049 ( 229 hom., cov: 32)

Consequence

ENSG00000310228
ENST00000848457.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.91

Publications

3 publications found

Variant links:

Genes affected

ENSG00000310228 (HGNC:):

ENSG00000310228 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=-0.98).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0719 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000310228	ENST00000848457.1 link	n.204+3531C>T	intron_variant	Intron 2 of 3
ENSG00000310228	ENST00000848458.1 link	n.185-1827C>T	intron_variant	Intron 2 of 3
ENSG00000310228	ENST00000848459.1 link	n.175+3531C>T	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.0491

AC:

7451

AN:

151832

Hom.:

228

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0740

Gnomad AMI

AF:

0.00877

Gnomad AMR

AF:

0.0624

Gnomad ASJ

AF:

0.0202

Gnomad EAS

AF:

0.00756

Gnomad SAS

AF:

0.00828

Gnomad FIN

AF:

0.0633

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.0370

Gnomad OTH

AF:

0.0445

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

GnomAD4 genome

AF:

0.0491

AC:

7462

AN:

151950

Hom.:

229

Cov.:

AF XY:

0.0507

AC XY:

3766

AN XY:

74262

show subpopulations

African (AFR)

AF:

0.0741

AC:

3076

AN:

41496

American (AMR)

AF:

0.0623

AC:

947

AN:

15206

Ashkenazi Jewish (ASJ)

AF:

0.0202

AC:

AN:

3466

East Asian (EAS)

AF:

0.00738

AC:

AN:

5150

South Asian (SAS)

AF:

0.00808

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.0633

AC:

672

AN:

10608

Middle Eastern (MID)

AF:

0.0238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0370

AC:

2512

AN:

67880

Other (OTH)

AF:

0.0440

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

357

714

1070

1427

1784

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

164

246

328

410

<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:

0.0395

Hom.:

230

Bravo

AF:

0.0506

Asia WGS

AF:

0.0310

AC:

108

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

2.0

(source)

DANN

Benign

0.45

PhyloP100

1.9

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