Variant rs2384953 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000585285.1(SLC9A3R1-AS1):n.340+129T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 156,114 control chromosomes in the GnomAD database, including 17,850 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.47 ( 17322 hom., cov: 32)

Exomes 𝑓: 0.48 ( 528 hom. )

Consequence

SLC9A3R1-AS1
ENST00000585285.1 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.761

Variant links:

Genes affected

SLC9A3R1-AS1 (HGNC:55322): (SLC9A3R1 antisense RNA 1)

SLC9A3R1-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 17-74748444-A-C is Benign according to our data. Variant chr17-74748444-A-C is described in ClinVar as [Benign]. Clinvar id is 1247073.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC9A3R1-AS1	NR_187307.1 link	n.1160+129T>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC9A3R1-AS1	ENST00000585285.1 link	n.340+129T>G		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes

AF:

0.472

AC:

71478

AN:

151438

Hom.:

17290

Cov.:

show subpopulations

Gnomad AFR

AF:

0.376

Gnomad AMI

AF:

0.313

Gnomad AMR

AF:

0.489

Gnomad ASJ

AF:

0.464

Gnomad EAS

AF:

0.448

Gnomad SAS

AF:

0.422

Gnomad FIN

AF:

0.571

Gnomad MID

AF:

0.442

Gnomad NFE

AF:

0.520

Gnomad OTH

AF:

0.456

GnomAD4 exome

AF:

0.485

AC:

2214

AN:

4568

Hom.:

528

AF XY:

0.484

AC XY:

1137

AN XY:

2348

show subpopulations

Gnomad4 AFR exome

AF:

0.380

Gnomad4 AMR exome

AF:

0.523

Gnomad4 ASJ exome

AF:

0.413

Gnomad4 EAS exome

AF:

0.453

Gnomad4 SAS exome

AF:

0.403

Gnomad4 FIN exome

AF:

0.574

Gnomad4 NFE exome

AF:

0.492

Gnomad4 OTH exome

AF:

0.483

GnomAD4 genome

AF:

0.472

AC:

71553

AN:

151546

Hom.:

17322

Cov.:

AF XY:

0.474

AC XY:

35141

AN XY:

74106

show subpopulations

Gnomad4 AFR

AF:

0.376

Gnomad4 AMR

AF:

0.489

Gnomad4 ASJ

AF:

0.464

Gnomad4 EAS

AF:

0.448

Gnomad4 SAS

AF:

0.422

Gnomad4 FIN

AF:

0.571

Gnomad4 NFE

AF:

0.520

Gnomad4 OTH

AF:

0.461

Alfa

AF:

0.411

Hom.:

1848

Bravo

AF:

0.468

Asia WGS

AF:

0.394

AC:

1339

AN:

3394

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Oct 16, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

9.6

DANN

Benign

0.32

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