dbSNP rs9262570: ENSG00000297077:n.90-1078C>T (chr6-31044708-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 ENST00000745182.1(ENSG00000297077):n.90-1078C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0252 in 152,262 control chromosomes in the GnomAD database, including 63 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 0.025 ( 63 hom., cov: 32)

Consequence

ENSG00000297077
ENST00000745182.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.509

Publications

8 publications found

Variant links:

Genes affected

ENSG00000297077 (HGNC:):

ENSG00000297077 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=-0.71).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0599 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
ENSG00000297077	ENST00000745182.1 link	n.90-1078C>T		intron_variant	Intron 1 of 1
ENSG00000297077	ENST00000745183.1 link	n.178-1078C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0252

AC:

3838

AN:

152144

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0316

Gnomad AMI

AF:

0.00548

Gnomad AMR

AF:

0.0232

Gnomad ASJ

AF:

0.0121

Gnomad EAS

AF:

0.0655

Gnomad SAS

AF:

0.0418

Gnomad FIN

AF:

0.00396

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.0216

Gnomad OTH

AF:

0.0316

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

GnomAD4 genome

AF:

0.0252

AC:

3843

AN:

152262

Hom.:

Cov.:

AF XY:

0.0255

AC XY:

1899

AN XY:

74448

show subpopulations

African (AFR)

AF:

0.0316

AC:

1314

AN:

41538

American (AMR)

AF:

0.0231

AC:

354

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.0121

AC:

AN:

3466

East Asian (EAS)

AF:

0.0656

AC:

340

AN:

5182

South Asian (SAS)

AF:

0.0421

AC:

203

AN:

4824

European-Finnish (FIN)

AF:

0.00396

AC:

AN:

10608

Middle Eastern (MID)

AF:

0.0272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0216

AC:

1469

AN:

68026

Other (OTH)

AF:

0.0313

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

197

393

590

786

983

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

150

200

250

<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:

0.0224

Hom.:

Bravo

AF:

0.0275

Asia WGS

AF:

0.0500

AC:

173

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

7.7

(source)

DANN

Benign

0.84

PhyloP100

-0.51

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