Variant 13-47629810-T-G 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 0.703 in 151,958 control chromosomes in the GnomAD database, including 37,870 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 0.70 ( 37870 hom., cov: 32)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.39

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.47629810T>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.703

AC:

106711

AN:

151840

Hom.:

37822

Cov.:

show subpopulations

Gnomad AFR

AF:

0.622

Gnomad AMI

AF:

0.765

Gnomad AMR

AF:

0.695

Gnomad ASJ

AF:

0.696

Gnomad EAS

AF:

0.661

Gnomad SAS

AF:

0.629

Gnomad FIN

AF:

0.717

Gnomad MID

AF:

0.753

Gnomad NFE

AF:

0.758

Gnomad OTH

AF:

0.725

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

GnomAD4 genome

AF:

0.703

AC:

106814

AN:

151958

Hom.:

37870

Cov.:

AF XY:

0.699

AC XY:

51909

AN XY:

74262

show subpopulations

Gnomad4 AFR

AF:

0.623

Gnomad4 AMR

AF:

0.695

Gnomad4 ASJ

AF:

0.696

Gnomad4 EAS

AF:

0.661

Gnomad4 SAS

AF:

0.630

Gnomad4 FIN

AF:

0.717

Gnomad4 NFE

AF:

0.758

Gnomad4 OTH

AF:

0.727

Alfa

AF:

0.697

Hom.:

3672

Bravo

AF:

0.701

Asia WGS

AF:

0.663

AC:

2303

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

DANN

Benign

0.88

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