dbSNP rs4949316: :null (chr1-30842746-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 0.616 in 152,138 control chromosomes in the GnomAD database, including 30,694 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 0.62 ( 30694 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.863

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=-0.91).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.731 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:

0.616

AC:

93706

AN:

152020

Hom.:

30680

Cov.:

show subpopulations

Gnomad AFR

AF:

0.383

Gnomad AMI

AF:

0.834

Gnomad AMR

AF:

0.742

Gnomad ASJ

AF:

0.649

Gnomad EAS

AF:

0.703

Gnomad SAS

AF:

0.572

Gnomad FIN

AF:

0.733

Gnomad MID

AF:

0.655

Gnomad NFE

AF:

0.703

Gnomad OTH

AF:

0.636

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

GnomAD4 genome

AF:

0.616

AC:

93740

AN:

152138

Hom.:

30694

Cov.:

AF XY:

0.620

AC XY:

46078

AN XY:

74374

show subpopulations

Gnomad4 AFR

AF:

0.382

Gnomad4 AMR

AF:

0.742

Gnomad4 ASJ

AF:

0.649

Gnomad4 EAS

AF:

0.704

Gnomad4 SAS

AF:

0.571

Gnomad4 FIN

AF:

0.733

Gnomad4 NFE

AF:

0.703

Gnomad4 OTH

AF:

0.638

Alfa

AF:

0.565

Hom.:

1833

Bravo

AF:

0.608

Asia WGS

AF:

0.602

AC:

2092

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

8.6

DANN

Benign

0.42

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