Variant 11-1267646-G-A 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 0.0731 in 290,254 control chromosomes in the GnomAD database, including 927 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 0.079 ( 513 hom., cov: 33)

Exomes 𝑓: 0.067 ( 414 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.702

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 (AMR) allele frequency at 95% confidence interval = 0.116 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:

0.0788

AC:

11991

AN:

152088

Hom.:

513

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0853

Gnomad AMI

AF:

0.0932

Gnomad AMR

AF:

0.120

Gnomad ASJ

AF:

0.0455

Gnomad EAS

AF:

0.00173

Gnomad SAS

AF:

0.0575

Gnomad FIN

AF:

0.103

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.0713

Gnomad OTH

AF:

0.0693

GnomAD4 exome

AF:

0.0668

AC:

9220

AN:

138048

Hom.:

414

AF XY:

0.0655

AC XY:

5001

AN XY:

76340

show subpopulations

Gnomad4 AFR exome

AF:

0.0828

Gnomad4 AMR exome

AF:

0.133

Gnomad4 ASJ exome

AF:

0.0360

Gnomad4 EAS exome

AF:

0.00127

Gnomad4 SAS exome

AF:

0.0595

Gnomad4 FIN exome

AF:

0.0801

Gnomad4 NFE exome

AF:

0.0683

Gnomad4 OTH exome

AF:

0.0651

GnomAD4 genome

AF:

0.0788

AC:

11997

AN:

152206

Hom.:

513

Cov.:

AF XY:

0.0812

AC XY:

6047

AN XY:

74436

show subpopulations

Gnomad4 AFR

AF:

0.0852

Gnomad4 AMR

AF:

0.120

Gnomad4 ASJ

AF:

0.0455

Gnomad4 EAS

AF:

0.00173

Gnomad4 SAS

AF:

0.0573

Gnomad4 FIN

AF:

0.103

Gnomad4 NFE

AF:

0.0713

Gnomad4 OTH

AF:

0.0686

Alfa

AF:

0.0774

Hom.:

Bravo

AF:

0.0814

Asia WGS

AF:

0.0310

AC:

109

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

6.7

DANN

Benign

0.23

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