dbSNP rs723147: ENSG00000298812:n.311-1273C>T (chr4-44544994-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000758081.1(ENSG00000298812):n.311-1273C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,100 control chromosomes in the GnomAD database, including 2,038 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 0.14 ( 2038 hom., cov: 32)

Consequence

ENSG00000298812
ENST00000758081.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.109

Publications

1 publications found

Variant links:

Genes affected

ENSG00000298812 (HGNC:):

ENSG00000298812 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 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
ENSG00000298812	ENST00000758081.1 link	n.311-1273C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.142

AC:

21531

AN:

151982

Hom.:

2038

Cov.:

show subpopulations

Gnomad AFR

AF:

0.273

Gnomad AMI

AF:

0.107

Gnomad AMR

AF:

0.0834

Gnomad ASJ

AF:

0.103

Gnomad EAS

AF:

0.103

Gnomad SAS

AF:

0.0704

Gnomad FIN

AF:

0.0796

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.0958

Gnomad OTH

AF:

0.121

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

GnomAD4 genome

AF:

0.142

AC:

21538

AN:

152100

Hom.:

2038

Cov.:

AF XY:

0.137

AC XY:

10173

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.273

AC:

11316

AN:

41440

American (AMR)

AF:

0.0832

AC:

1271

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.103

AC:

358

AN:

3472

East Asian (EAS)

AF:

0.103

AC:

533

AN:

5182

South Asian (SAS)

AF:

0.0692

AC:

334

AN:

4824

European-Finnish (FIN)

AF:

0.0796

AC:

843

AN:

10592

Middle Eastern (MID)

AF:

0.0544

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0958

AC:

6514

AN:

68002

Other (OTH)

AF:

0.121

AC:

255

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

892

1784

2675

3567

4459

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

222

444

666

888

1110

<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:

0.132

Hom.:

240

Bravo

AF:

0.147

Asia WGS

AF:

0.111

AC:

388

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.1

(source)

DANN

Benign

0.47

PhyloP100

0.11

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