dbSNP rs1835482: :null (chr8-72393439-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.3 in 152,122 control chromosomes in the GnomAD database, including 7,114 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 0.30 ( 7114 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.241

Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BA1

GnomAd4 highest subpopulation (SAS) 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

Frequencies

GnomAD3 genomes

AF:

0.300

AC:

45624

AN:

152004

Hom.:

7113

Cov.:

show subpopulations

Gnomad AFR

AF:

0.226

Gnomad AMI

AF:

0.364

Gnomad AMR

AF:

0.259

Gnomad ASJ

AF:

0.373

Gnomad EAS

AF:

0.165

Gnomad SAS

AF:

0.378

Gnomad FIN

AF:

0.292

Gnomad MID

AF:

0.497

Gnomad NFE

AF:

0.354

Gnomad OTH

AF:

0.325

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

GnomAD4 genome

AF:

0.300

AC:

45635

AN:

152122

Hom.:

7114

Cov.:

AF XY:

0.297

AC XY:

22094

AN XY:

74362

show subpopulations

Gnomad4 AFR

AF:

0.226

Gnomad4 AMR

AF:

0.259

Gnomad4 ASJ

AF:

0.373

Gnomad4 EAS

AF:

0.166

Gnomad4 SAS

AF:

0.380

Gnomad4 FIN

AF:

0.292

Gnomad4 NFE

AF:

0.354

Gnomad4 OTH

AF:

0.324

Alfa

AF:

0.318

Hom.:

993

Bravo

AF:

0.290

Asia WGS

AF:

0.281

AC:

978

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

1.5

DANN

Benign

0.44

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over