dbSNP rs2740209: :null (chr20-3072850-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 0.27 in 152,184 control chromosomes in the GnomAD database, including 6,118 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 0.27 ( 6118 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.712

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=-0.92).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.37 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:

0.270

AC:

41013

AN:

152066

Hom.:

6105

Cov.:

show subpopulations

Gnomad AFR

AF:

0.151

Gnomad AMI

AF:

0.109

Gnomad AMR

AF:

0.377

Gnomad ASJ

AF:

0.291

Gnomad EAS

AF:

0.270

Gnomad SAS

AF:

0.270

Gnomad FIN

AF:

0.265

Gnomad MID

AF:

0.247

Gnomad NFE

AF:

0.320

Gnomad OTH

AF:

0.254

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

GnomAD4 genome

AF:

0.270

AC:

41049

AN:

152184

Hom.:

6118

Cov.:

AF XY:

0.269

AC XY:

20010

AN XY:

74380

show subpopulations

Gnomad4 AFR

AF:

0.151

Gnomad4 AMR

AF:

0.378

Gnomad4 ASJ

AF:

0.291

Gnomad4 EAS

AF:

0.270

Gnomad4 SAS

AF:

0.271

Gnomad4 FIN

AF:

0.265

Gnomad4 NFE

AF:

0.320

Gnomad4 OTH

AF:

0.255

Alfa

AF:

0.177

Hom.:

394

Bravo

AF:

0.276

Asia WGS

AF:

0.309

AC:

1075

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

3.4

DANN

Benign

0.67

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