dbSNP rs619788: :null (chr15-34702905-C-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 0.497 in 152,082 control chromosomes in the GnomAD database, including 19,851 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 0.50 ( 19851 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.420

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=-0.67).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.671 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:

0.497

AC:

75500

AN:

151964

Hom.:

19817

Cov.:

show subpopulations

Gnomad AFR

AF:

0.677

Gnomad AMI

AF:

0.654

Gnomad AMR

AF:

0.409

Gnomad ASJ

AF:

0.385

Gnomad EAS

AF:

0.439

Gnomad SAS

AF:

0.590

Gnomad FIN

AF:

0.348

Gnomad MID

AF:

0.335

Gnomad NFE

AF:

0.433

Gnomad OTH

AF:

0.467

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

GnomAD4 genome

AF:

0.497

AC:

75590

AN:

152082

Hom.:

19851

Cov.:

AF XY:

0.492

AC XY:

36532

AN XY:

74324

show subpopulations

Gnomad4 AFR

AF:

0.677

Gnomad4 AMR

AF:

0.408

Gnomad4 ASJ

AF:

0.385

Gnomad4 EAS

AF:

0.439

Gnomad4 SAS

AF:

0.589

Gnomad4 FIN

AF:

0.348

Gnomad4 NFE

AF:

0.433

Gnomad4 OTH

AF:

0.468

Alfa

AF:

0.277

Hom.:

591

Bravo

AF:

0.505

Asia WGS

AF:

0.542

AC:

1883

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

1.4

DANN

Benign

0.78

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