Variant rs10501828 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 0.612 in 152,196 control chromosomes in the GnomAD database, including 30,222 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 0.61 ( 30222 hom., cov: 33)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.958

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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.95511045G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.612

AC:

93093

AN:

152078

Hom.:

30171

Cov.:

show subpopulations

Gnomad AFR

AF:

0.829

Gnomad AMI

AF:

0.399

Gnomad AMR

AF:

0.643

Gnomad ASJ

AF:

0.615

Gnomad EAS

AF:

0.629

Gnomad SAS

AF:

0.582

Gnomad FIN

AF:

0.461

Gnomad MID

AF:

0.636

Gnomad NFE

AF:

0.500

Gnomad OTH

AF:

0.616

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

GnomAD4 genome

AF:

0.612

AC:

93208

AN:

152196

Hom.:

30222

Cov.:

AF XY:

0.612

AC XY:

45541

AN XY:

74414

show subpopulations

Gnomad4 AFR

AF:

0.830

Gnomad4 AMR

AF:

0.644

Gnomad4 ASJ

AF:

0.615

Gnomad4 EAS

AF:

0.629

Gnomad4 SAS

AF:

0.582

Gnomad4 FIN

AF:

0.461

Gnomad4 NFE

AF:

0.500

Gnomad4 OTH

AF:

0.614

Alfa

AF:

0.487

Hom.:

2379

Bravo

AF:

0.636

Asia WGS

AF:

0.639

AC:

2218

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.11

DANN

Benign

0.41

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