Variant 20-44318326-T-G 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 0.301 in 152,014 control chromosomes in the GnomAD database, including 8,420 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 0.30 ( 8420 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.40

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=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.461 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:

0.301

AC:

45706

AN:

151896

Hom.:

8381

Cov.:

show subpopulations

Gnomad AFR

AF:

0.466

Gnomad AMI

AF:

0.163

Gnomad AMR

AF:

0.419

Gnomad ASJ

AF:

0.251

Gnomad EAS

AF:

0.458

Gnomad SAS

AF:

0.414

Gnomad FIN

AF:

0.228

Gnomad MID

AF:

0.288

Gnomad NFE

AF:

0.170

Gnomad OTH

AF:

0.300

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

GnomAD4 genome

AF:

0.301

AC:

45809

AN:

152014

Hom.:

8420

Cov.:

AF XY:

0.308

AC XY:

22895

AN XY:

74324

show subpopulations

Gnomad4 AFR

AF:

0.466

Gnomad4 AMR

AF:

0.420

Gnomad4 ASJ

AF:

0.251

Gnomad4 EAS

AF:

0.458

Gnomad4 SAS

AF:

0.416

Gnomad4 FIN

AF:

0.228

Gnomad4 NFE

AF:

0.170

Gnomad4 OTH

AF:

0.303

Alfa

AF:

0.216

Hom.:

1240

Bravo

AF:

0.323

Asia WGS

AF:

0.446

AC:

1548

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.74

DANN

Benign

0.80

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