Variant rs1642210 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 0.856 in 152,162 control chromosomes in the GnomAD database, including 57,048 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 0.86 ( 57048 hom., cov: 32)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.345

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=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.86981142C>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000259061	ENST00000554181.1 linkuse as main transcript	n.189-6846C>A		intron_variant		2

Frequencies

GnomAD3 genomes

AF:

0.856

AC:

130201

AN:

152044

Hom.:

57025

Cov.:

show subpopulations

Gnomad AFR

AF:

0.665

Gnomad AMI

AF:

0.948

Gnomad AMR

AF:

0.816

Gnomad ASJ

AF:

0.932

Gnomad EAS

AF:

0.791

Gnomad SAS

AF:

0.908

Gnomad FIN

AF:

0.979

Gnomad MID

AF:

0.915

Gnomad NFE

AF:

0.958

Gnomad OTH

AF:

0.880

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

GnomAD4 genome

AF:

0.856

AC:

130269

AN:

152162

Hom.:

57048

Cov.:

AF XY:

0.856

AC XY:

63701

AN XY:

74420

show subpopulations

Gnomad4 AFR

AF:

0.665

Gnomad4 AMR

AF:

0.816

Gnomad4 ASJ

AF:

0.932

Gnomad4 EAS

AF:

0.790

Gnomad4 SAS

AF:

0.910

Gnomad4 FIN

AF:

0.979

Gnomad4 NFE

AF:

0.958

Gnomad4 OTH

AF:

0.882

Alfa

AF:

0.929

Hom.:

28097

Bravo

AF:

0.834

Asia WGS

AF:

0.831

AC:

2891

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

4.4

DANN

Benign

0.70

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