dbSNP rs2307924: ENSG00000285718:n.250+11241_250+11242insTATTTAAT (chr1-194909217-G-GATTAAATA) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000648938.1(ENSG00000285718):n.250+11241_250+11242insTATTTAAT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.53 ( 21485 hom., cov: 0)

Consequence

ENSG00000285718
ENST00000648938.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.618

Publications

4 publications found

Variant links:

Genes affected

ENSG00000285718 (HGNC:):

ENSG00000285718 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.659 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
ENSG00000285718	ENST00000648938.1 link	n.250+11241_250+11242insTATTTAAT		intron_variant	Intron 2 of 3
ENSG00000285718	ENST00000670710.1 link	n.216+11241_216+11242insTATTTAAT		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.525

AC:

79327

AN:

151054

Hom.:

21450

Cov.:

show subpopulations

Gnomad AFR

AF:

0.665

Gnomad AMI

AF:

0.354

Gnomad AMR

AF:

0.443

Gnomad ASJ

AF:

0.481

Gnomad EAS

AF:

0.315

Gnomad SAS

AF:

0.491

Gnomad FIN

AF:

0.561

Gnomad MID

AF:

0.477

Gnomad NFE

AF:

0.477

Gnomad OTH

AF:

0.505

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

GnomAD4 genome

AF:

0.525

AC:

79411

AN:

151174

Hom.:

21485

Cov.:

AF XY:

0.525

AC XY:

38739

AN XY:

73806

show subpopulations

African (AFR)

AF:

0.665

AC:

27436

AN:

41250

American (AMR)

AF:

0.442

AC:

6696

AN:

15140

Ashkenazi Jewish (ASJ)

AF:

0.481

AC:

1658

AN:

3444

East Asian (EAS)

AF:

0.316

AC:

1623

AN:

5140

South Asian (SAS)

AF:

0.491

AC:

2348

AN:

4784

European-Finnish (FIN)

AF:

0.561

AC:

5876

AN:

10468

Middle Eastern (MID)

AF:

0.479

AC:

139

AN:

290

European-Non Finnish (NFE)

AF:

0.477

AC:

32249

AN:

67652

Other (OTH)

AF:

0.507

AC:

1066

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1854

3707

5561

7414

9268

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

700

1400

2100

2800

3500

<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:

0.340

Hom.:

650

Asia WGS

AF:

0.414

AC:

1439

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.62

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