Variant rs2267864 details in Genebe, Genetics Data Aggregator

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 0.199 in 158,766 control chromosomes in the GnomAD database, including 3,232 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 0.20 ( 3115 hom., cov: 32)

Exomes 𝑓: 0.16 ( 117 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.577

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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.201

AC:

30476

AN:

151766

Hom.:

3102

Cov.:

show subpopulations

Gnomad AFR

AF:

0.220

Gnomad AMI

AF:

0.316

Gnomad AMR

AF:

0.200

Gnomad ASJ

AF:

0.204

Gnomad EAS

AF:

0.101

Gnomad SAS

AF:

0.154

Gnomad FIN

AF:

0.235

Gnomad MID

AF:

0.244

Gnomad NFE

AF:

0.193

Gnomad OTH

AF:

0.204

GnomAD4 exome

AF:

0.163

AC:

1122

AN:

6882

Hom.:

117

AF XY:

0.168

AC XY:

621

AN XY:

3692

show subpopulations

Gnomad4 AFR exome

AF:

0.182

Gnomad4 AMR exome

AF:

0.160

Gnomad4 ASJ exome

AF:

0.0909

Gnomad4 EAS exome

AF:

0.103

Gnomad4 SAS exome

AF:

0.160

Gnomad4 FIN exome

AF:

0.200

Gnomad4 NFE exome

AF:

0.167

Gnomad4 OTH exome

AF:

0.162

GnomAD4 genome

AF:

0.201

AC:

30540

AN:

151884

Hom.:

3115

Cov.:

AF XY:

0.204

AC XY:

15110

AN XY:

74216

show subpopulations

Gnomad4 AFR

AF:

0.220

Gnomad4 AMR

AF:

0.200

Gnomad4 ASJ

AF:

0.204

Gnomad4 EAS

AF:

0.101

Gnomad4 SAS

AF:

0.156

Gnomad4 FIN

AF:

0.235

Gnomad4 NFE

AF:

0.193

Gnomad4 OTH

AF:

0.207

Alfa

AF:

0.0981

Hom.:

137

Bravo

AF:

0.200

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

4.5

DANN

Benign

0.43

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