Variant rs7173049 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 0.22 in 161,388 control chromosomes in the GnomAD database, including 4,095 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.22 ( 3860 hom., cov: 33)

Exomes 𝑓: 0.22 ( 235 hom. )

Consequence

Unknown

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.308

Variant links:

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ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 15-73952269-A-G is Benign according to our data. Variant chr15-73952269-A-G is described in ClinVar as [Benign]. Clinvar id is 1266506.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.371 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:

0.220

AC:

33425

AN:

151978

Hom.:

3847

Cov.:

show subpopulations

Gnomad AFR

AF:

0.232

Gnomad AMI

AF:

0.211

Gnomad AMR

AF:

0.171

Gnomad ASJ

AF:

0.248

Gnomad EAS

AF:

0.290

Gnomad SAS

AF:

0.386

Gnomad FIN

AF:

0.185

Gnomad MID

AF:

0.263

Gnomad NFE

AF:

0.210

Gnomad OTH

AF:

0.239

GnomAD4 exome

AF:

0.216

AC:

2003

AN:

9292

Hom.:

235

AF XY:

0.206

AC XY:

985

AN XY:

4772

show subpopulations

Gnomad4 AFR exome

AF:

0.226

Gnomad4 AMR exome

AF:

0.167

Gnomad4 ASJ exome

AF:

0.198

Gnomad4 EAS exome

AF:

0.314

Gnomad4 SAS exome

AF:

0.412

Gnomad4 FIN exome

AF:

0.185

Gnomad4 NFE exome

AF:

0.206

Gnomad4 OTH exome

AF:

0.238

GnomAD4 genome

AF:

0.220

AC:

33470

AN:

152096

Hom.:

3860

Cov.:

AF XY:

0.223

AC XY:

16561

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.232

Gnomad4 AMR

AF:

0.171

Gnomad4 ASJ

AF:

0.248

Gnomad4 EAS

AF:

0.290

Gnomad4 SAS

AF:

0.386

Gnomad4 FIN

AF:

0.185

Gnomad4 NFE

AF:

0.210

Gnomad4 OTH

AF:

0.246

Alfa

AF:

0.211

Hom.:

4763

Bravo

AF:

0.217

Asia WGS

AF:

0.363

AC:

1263

AN:

3478

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

Oct 16, 2019

This variant is associated with the following publications: (PMID: 30986821) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.6

DANN

Benign

0.35

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