Variant chr4-167915543-A-T 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 0.279 in 152,068 control chromosomes in the GnomAD database, including 6,558 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 0.28 ( 6558 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.517

Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.279

AC:

42333

AN:

151950

Hom.:

6552

Cov.:

show subpopulations

Gnomad AFR

AF:

0.387

Gnomad AMI

AF:

0.293

Gnomad AMR

AF:

0.211

Gnomad ASJ

AF:

0.307

Gnomad EAS

AF:

0.0952

Gnomad SAS

AF:

0.138

Gnomad FIN

AF:

0.161

Gnomad MID

AF:

0.310

Gnomad NFE

AF:

0.268

Gnomad OTH

AF:

0.296

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

GnomAD4 genome

AF:

0.279

AC:

42362

AN:

152068

Hom.:

6558

Cov.:

AF XY:

0.269

AC XY:

20016

AN XY:

74338

show subpopulations

Gnomad4 AFR

AF:

0.387

Gnomad4 AMR

AF:

0.211

Gnomad4 ASJ

AF:

0.307

Gnomad4 EAS

AF:

0.0956

Gnomad4 SAS

AF:

0.139

Gnomad4 FIN

AF:

0.161

Gnomad4 NFE

AF:

0.268

Gnomad4 OTH

AF:

0.293

Alfa

AF:

0.269

Hom.:

748

Bravo

AF:

0.289

Asia WGS

AF:

0.120

AC:

417

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.52

DANN

Benign

0.62

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