chr17-74748473-G-A

Variant names:

• chr17-74748473-G-A
• rs2084313
• ENST00000585285.1:n.340+100C>T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BS1 BS2

The ENST00000585285.1(SLC9A3R1-AS1):​n.340+100C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0198 in 166,078 control chromosomes in the GnomAD database, including 43 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.020 (38 hom., cov: 34)
  • Exomes 𝑓: 0.019 (5 hom.)
• Consequence: SLC9A3R1-AS1 ENST00000585285.1 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.784

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=-0.73).
• BP6: Variant 17-74748473-G-A is Benign according to our data. Variant chr17-74748473-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1316461.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0199 (3028/151912) while in subpopulation SAS AF= 0.0352 (170/4830). AF 95% confidence interval is 0.0309. There are 38 homozygotes in gnomad4. There are 1508 alleles in male gnomad4 subpopulation. Median coverage is 34. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 38 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC9A3R1-AS1	NR_187307.1	n.1160+100C>T		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+100C>T		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.0199 AC: 3024 AN: 151804 Hom.: 38 Cov.: 34

Gnomad AFR AF: 0.0210

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0262

Gnomad ASJ AF: 0.0412

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0350

Gnomad FIN AF: 0.0193

Gnomad MID AF: 0.0510

Gnomad NFE AF: 0.0173

Gnomad OTH AF: 0.0240

GnomAD4 exome AF: 0.0188 AC: 267 AN: 14166 Hom.: 5 AF XY: 0.0221 AC XY: 158 AN XY: 7160

Gnomad4 AFR exome AF: 0.0272

Gnomad4 AMR exome AF: 0.0133

Gnomad4 ASJ exome AF: 0.0441

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0305

Gnomad4 FIN exome AF: 0.0177

Gnomad4 NFE exome AF: 0.0177

Gnomad4 OTH exome AF: 0.0266

GnomAD4 genome AF: 0.0199 AC: 3028 AN: 151912 Hom.: 38 Cov.: 34 AF XY: 0.0203 AC XY: 1508 AN XY: 74262

Gnomad4 AFR AF: 0.0210

Gnomad4 AMR AF: 0.0262

Gnomad4 ASJ AF: 0.0412

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0352

Gnomad4 FIN AF: 0.0193

Gnomad4 NFE AF: 0.0173

Gnomad4 OTH AF: 0.0237

Alfa AF: 0.00556 Hom.: 0

Bravo AF: 0.0198

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Oct 07, 2019

GeneDx

Significance: Likely 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	-0.73
CADD	Benign	6.8
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2084313; hg19: chr17-72744612;