Variant chr7-33062850-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The variant allele was found at a frequency of 0.694 in 1,413,142 control chromosomes in the GnomAD database, including 342,867 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.69 ( 36292 hom., cov: 32)

Exomes 𝑓: 0.69 ( 306575 hom. )

Consequence

intergenic_region

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.423

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP6

Variant 7-33062850-C-T is Benign according to our data. Variant chr7-33062850-C-T is described in ClinVar as [Benign]. Clinvar id is 1257930.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.33062850C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.692

AC:

104490

AN:

151106

Hom.:

36252

Cov.:

show subpopulations

Gnomad AFR

AF:

0.699

Gnomad AMI

AF:

0.502

Gnomad AMR

AF:

0.720

Gnomad ASJ

AF:

0.561

Gnomad EAS

AF:

0.492

Gnomad SAS

AF:

0.603

Gnomad FIN

AF:

0.759

Gnomad MID

AF:

0.608

Gnomad NFE

AF:

0.702

Gnomad OTH

AF:

0.665

GnomAD4 exome

AF:

0.694

AC:

876078

AN:

1261920

Hom.:

306575

AF XY:

0.691

AC XY:

433736

AN XY:

628092

show subpopulations

Gnomad4 AFR exome

AF:

0.703

Gnomad4 AMR exome

AF:

0.759

Gnomad4 ASJ exome

AF:

0.559

Gnomad4 EAS exome

AF:

0.498

Gnomad4 SAS exome

AF:

0.610

Gnomad4 FIN exome

AF:

0.757

Gnomad4 NFE exome

AF:

0.708

Gnomad4 OTH exome

AF:

0.670

GnomAD4 genome

AF:

0.692

AC:

104584

AN:

151222

Hom.:

36292

Cov.:

AF XY:

0.693

AC XY:

51198

AN XY:

73930

show subpopulations

Gnomad4 AFR

AF:

0.699

Gnomad4 AMR

AF:

0.720

Gnomad4 ASJ

AF:

0.561

Gnomad4 EAS

AF:

0.491

Gnomad4 SAS

AF:

0.605

Gnomad4 FIN

AF:

0.759

Gnomad4 NFE

AF:

0.702

Gnomad4 OTH

AF:

0.660

Alfa

AF:

0.617

Hom.:

1829

Bravo

AF:

0.686

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

7.6

DANN

Benign

0.93

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over