ENST00000585285.1:n.340+200A>G

Variant names:

• chr17-74748373-T-C
• rs2384952
• ENST00000585285.1:n.340+200A>G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000585285.1(SLC9A3R1-AS1):​n.340+200A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 151,918 control chromosomes in the GnomAD database, including 17,883 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.48 (17883 hom., cov: 33)
• Consequence: SLC9A3R1-AS1 ENST00000585285.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.600

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BP6: Variant 17-74748373-T-C is Benign according to our data. Variant chr17-74748373-T-C is described in ClinVar as [Benign]. Clinvar id is 1265446.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC9A3R1-AS1	NR_187307.1	n.1160+200A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC9A3R1-AS1	ENST00000585285.1	n.340+200A>G		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72719 AN: 151810 Hom.: 17850 Cov.: 33

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.479 AC: 72796 AN: 151918 Hom.: 17883 Cov.: 33 AF XY: 0.481 AC XY: 35711 AN XY: 74240

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.447

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.528

Gnomad4 OTH AF: 0.464

Alfa AF: 0.498 Hom.: 2716

Bravo AF: 0.475

Asia WGS AF: 0.387 AC: 1335 AN: 3444

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

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	-0.76
CADD	Benign	12
DANN	Benign	0.63

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2384952; hg19: chr17-72744512;