dbSNP rs7838658: ENSG00000288782:n.213-9387G>A (chr8-2217043-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 ENST00000776947.1(ENSG00000288782):n.213-9387G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 152,048 control chromosomes in the GnomAD database, including 7,860 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 0.32 ( 7860 hom., cov: 32)

Consequence

ENSG00000288782
ENST00000776947.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.35

Publications

3 publications found

Variant links:

Genes affected

ENSG00000288782 (HGNC:):

ENSG00000288782 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=-1.03).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.365 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
ENSG00000288782	ENST00000776947.1 link	n.213-9387G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.316

AC:

47994

AN:

151930

Hom.:

7860

Cov.:

show subpopulations

Gnomad AFR

AF:

0.370

Gnomad AMI

AF:

0.245

Gnomad AMR

AF:

0.261

Gnomad ASJ

AF:

0.287

Gnomad EAS

AF:

0.262

Gnomad SAS

AF:

0.148

Gnomad FIN

AF:

0.336

Gnomad MID

AF:

0.278

Gnomad NFE

AF:

0.312

Gnomad OTH

AF:

0.292

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

GnomAD4 genome

AF:

0.316

AC:

48026

AN:

152048

Hom.:

7860

Cov.:

AF XY:

0.312

AC XY:

23167

AN XY:

74300

show subpopulations

African (AFR)

AF:

0.370

AC:

15329

AN:

41474

American (AMR)

AF:

0.261

AC:

3993

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.287

AC:

992

AN:

3458

East Asian (EAS)

AF:

0.263

AC:

1355

AN:

5148

South Asian (SAS)

AF:

0.148

AC:

712

AN:

4820

European-Finnish (FIN)

AF:

0.336

AC:

3557

AN:

10592

Middle Eastern (MID)

AF:

0.276

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.312

AC:

21177

AN:

67950

Other (OTH)

AF:

0.288

AC:

607

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1677

3354

5031

6708

8385

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

486

972

1458

1944

2430

<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:

0.305

Hom.:

7422

Bravo

AF:

0.316

Asia WGS

AF:

0.189

AC:

658

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.7

(source)

DANN

Benign

0.60

PhyloP100

-1.4

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