Variant rs7272098 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 0.354 in 152,070 control chromosomes in the GnomAD database, including 9,961 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 0.35 ( 9961 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.315

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=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.642 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:

0.354

AC:

53804

AN:

151952

Hom.:

9945

Cov.:

show subpopulations

Gnomad AFR

AF:

0.287

Gnomad AMI

AF:

0.456

Gnomad AMR

AF:

0.345

Gnomad ASJ

AF:

0.185

Gnomad EAS

AF:

0.660

Gnomad SAS

AF:

0.407

Gnomad FIN

AF:

0.415

Gnomad MID

AF:

0.165

Gnomad NFE

AF:

0.369

Gnomad OTH

AF:

0.331

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

GnomAD4 genome

AF:

0.354

AC:

53854

AN:

152070

Hom.:

9961

Cov.:

AF XY:

0.358

AC XY:

26622

AN XY:

74308

show subpopulations

Gnomad4 AFR

AF:

0.287

Gnomad4 AMR

AF:

0.346

Gnomad4 ASJ

AF:

0.185

Gnomad4 EAS

AF:

0.661

Gnomad4 SAS

AF:

0.406

Gnomad4 FIN

AF:

0.415

Gnomad4 NFE

AF:

0.369

Gnomad4 OTH

AF:

0.335

Alfa

AF:

0.362

Hom.:

1272

Bravo

AF:

0.347

Asia WGS

AF:

0.425

AC:

1473

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

3.5

DANN

Benign

0.77

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