dbSNP rs835154: :null (chr5-14876460-G-A) – 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 0.648 in 152,034 control chromosomes in the GnomAD database, including 33,615 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 0.65 ( 33615 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.565

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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.869 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:

0.648

AC:

98454

AN:

151916

Hom.:

33546

Cov.:

show subpopulations

Gnomad AFR

AF:

0.876

Gnomad AMI

AF:

0.413

Gnomad AMR

AF:

0.555

Gnomad ASJ

AF:

0.537

Gnomad EAS

AF:

0.683

Gnomad SAS

AF:

0.604

Gnomad FIN

AF:

0.599

Gnomad MID

AF:

0.500

Gnomad NFE

AF:

0.549

Gnomad OTH

AF:

0.611

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

GnomAD4 genome

AF:

0.648

AC:

98590

AN:

152034

Hom.:

33615

Cov.:

AF XY:

0.647

AC XY:

48096

AN XY:

74292

show subpopulations

Gnomad4 AFR

AF:

0.877

Gnomad4 AMR

AF:

0.555

Gnomad4 ASJ

AF:

0.537

Gnomad4 EAS

AF:

0.683

Gnomad4 SAS

AF:

0.605

Gnomad4 FIN

AF:

0.599

Gnomad4 NFE

AF:

0.549

Gnomad4 OTH

AF:

0.616

Alfa

AF:

0.617

Hom.:

7225

Bravo

AF:

0.655

Asia WGS

AF:

0.671

AC:

2335

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

DANN

Benign

0.65

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