Genetic Variant ENSG00000298854:n.70+4870T>C (chr6-110977022-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 ENST00000758433.1(ENSG00000298854):n.70+4870T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 152,106 control chromosomes in the GnomAD database, including 5,387 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 0.25 ( 5387 hom., cov: 33)

Consequence

ENSG00000298854
ENST00000758433.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.342

Publications

4 publications found

Variant links:

Genes affected

ENSG00000298854 (HGNC:):

ENSG00000298854 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=-1.01).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.633 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
ENSG00000298854	ENST00000758433.1 link	n.70+4870T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.248

AC:

37619

AN:

151988

Hom.:

5388

Cov.:

show subpopulations

Gnomad AFR

AF:

0.320

Gnomad AMI

AF:

0.247

Gnomad AMR

AF:

0.157

Gnomad ASJ

AF:

0.144

Gnomad EAS

AF:

0.652

Gnomad SAS

AF:

0.347

Gnomad FIN

AF:

0.296

Gnomad MID

AF:

0.127

Gnomad NFE

AF:

0.185

Gnomad OTH

AF:

0.222

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

GnomAD4 genome

AF:

0.247

AC:

37640

AN:

152106

Hom.:

5387

Cov.:

AF XY:

0.254

AC XY:

18911

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.320

AC:

13276

AN:

41486

American (AMR)

AF:

0.157

AC:

2391

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.144

AC:

501

AN:

3470

East Asian (EAS)

AF:

0.652

AC:

3370

AN:

5170

South Asian (SAS)

AF:

0.345

AC:

1663

AN:

4822

European-Finnish (FIN)

AF:

0.296

AC:

3127

AN:

10574

Middle Eastern (MID)

AF:

0.139

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.185

AC:

12566

AN:

67992

Other (OTH)

AF:

0.227

AC:

480

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

1409

2819

4228

5638

7047

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

388

776

1164

1552

1940

<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:

0.223

Hom.:

737

Bravo

AF:

0.234

Asia WGS

AF:

0.477

AC:

1660

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

2.6

(source)

DANN

Benign

0.65

PhyloP100

-0.34

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