Variant 7-30931374-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 0.215 in 152,150 control chromosomes in the GnomAD database, including 3,727 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 0.21 ( 3727 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.328

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=-0.85).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.255 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:

0.215

AC:

32653

AN:

152032

Hom.:

3724

Cov.:

show subpopulations

Gnomad AFR

AF:

0.154

Gnomad AMI

AF:

0.130

Gnomad AMR

AF:

0.236

Gnomad ASJ

AF:

0.252

Gnomad EAS

AF:

0.100

Gnomad SAS

AF:

0.267

Gnomad FIN

AF:

0.182

Gnomad MID

AF:

0.320

Gnomad NFE

AF:

0.255

Gnomad OTH

AF:

0.241

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

GnomAD4 genome

AF:

0.215

AC:

32672

AN:

152150

Hom.:

3727

Cov.:

AF XY:

0.213

AC XY:

15839

AN XY:

74374

show subpopulations

Gnomad4 AFR

AF:

0.154

Gnomad4 AMR

AF:

0.236

Gnomad4 ASJ

AF:

0.252

Gnomad4 EAS

AF:

0.101

Gnomad4 SAS

AF:

0.267

Gnomad4 FIN

AF:

0.182

Gnomad4 NFE

AF:

0.255

Gnomad4 OTH

AF:

0.243

Alfa

AF:

0.244

Hom.:

6396

Bravo

AF:

0.215

Asia WGS

AF:

0.237

AC:

822

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

2.0

DANN

Benign

0.78

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