17-74748444-A-C

Variant names:

• chr17-74748444-A-C
• rs2384953
• ENST00000585285.1:n.340+129T>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+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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.761

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=-0.82).
• 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	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	n.340+129T>G		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71478 AN: 151438 Hom.: 17290 Cov.: 32

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

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.: 32 AF XY: 0.474 AC XY: 35141 AN XY: 74106

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

Submissions by phenotype

not provided Benign:1

Oct 16, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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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

Other links and lift over

dbSNP: rs2384953; hg19: chr17-72744583;