Variant 6-31218757-C-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 0.219 in 151,964 control chromosomes in the GnomAD database, including 3,927 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 0.22 ( 3927 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.48

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=-1.01).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.249 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:

0.219

AC:

33185

AN:

151848

Hom.:

3924

Cov.:

show subpopulations

Gnomad AFR

AF:

0.148

Gnomad AMI

AF:

0.340

Gnomad AMR

AF:

0.256

Gnomad ASJ

AF:

0.422

Gnomad EAS

AF:

0.125

Gnomad SAS

AF:

0.231

Gnomad FIN

AF:

0.273

Gnomad MID

AF:

0.323

Gnomad NFE

AF:

0.237

Gnomad OTH

AF:

0.274

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

GnomAD4 genome

AF:

0.219

AC:

33208

AN:

151964

Hom.:

3927

Cov.:

AF XY:

0.221

AC XY:

16405

AN XY:

74242

show subpopulations

Gnomad4 AFR

AF:

0.148

Gnomad4 AMR

AF:

0.256

Gnomad4 ASJ

AF:

0.422

Gnomad4 EAS

AF:

0.125

Gnomad4 SAS

AF:

0.231

Gnomad4 FIN

AF:

0.273

Gnomad4 NFE

AF:

0.237

Gnomad4 OTH

AF:

0.274

Alfa

AF:

0.246

Hom.:

3149

Bravo

AF:

0.217

Asia WGS

AF:

0.193

AC:

671

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

3.2

DANN

Benign

0.31

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