9-137618895-A-G

Position:

• chr9-137618895-A-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NR_122035.1(ARRDC1-AS1):​n.1T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0248 in 311,110 control chromosomes in the GnomAD database, including 576 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.047 (527 hom., cov: 32)
  • Exomes 𝑓: 0.0041 (49 hom.)
• Consequence: ARRDC1-AS1 NR_122035.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.177

Genes affected

ARRDC1-AS1 (HGNC:23395): (ARRDC1 antisense RNA 1) This transcribed locus is thought to be non-coding. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2014]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 9-137618895-A-G is Benign according to our data. Variant chr9-137618895-A-G is described in ClinVar as [Benign]. Clinvar id is 1259050.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARRDC1-AS1	NR_122035.1	n.1T>C		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARRDC1-AS1	ENST00000496793.3	n.12T>C		non_coding_transcript_exon_variant	1/2	2
ARRDC1-AS1	ENST00000371417.4			upstream_gene_variant		1
ARRDC1-AS1	ENST00000663398.2			upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0469 AC: 7056 AN: 150478 Hom.: 525 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0178

Gnomad ASJ AF: 0.000289

Gnomad EAS AF: 0.00373

Gnomad SAS AF: 0.00124

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00968

Gnomad NFE AF: 0.000726

Gnomad OTH AF: 0.0411

GnomAD4 exome AF: 0.00408 AC: 655 AN: 160530 Hom.: 49 Cov.: 3 AF XY: 0.00390 AC XY: 295 AN XY: 75674

Gnomad4 AFR exome AF: 0.164

Gnomad4 AMR exome AF: 0.00350

Gnomad4 ASJ exome AF: 0.00101

Gnomad4 EAS exome AF: 0.00257

Gnomad4 SAS exome AF: 0.000306

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000137

Gnomad4 OTH exome AF: 0.0136

GnomAD4 genome AF: 0.0470 AC: 7073 AN: 150580 Hom.: 527 Cov.: 32 AF XY: 0.0457 AC XY: 3361 AN XY: 73526

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.0177

Gnomad4 ASJ AF: 0.000289

Gnomad4 EAS AF: 0.00374

Gnomad4 SAS AF: 0.00104

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000726

Gnomad4 OTH AF: 0.0407

Alfa AF: 0.000501 Hom.: 0

Asia WGS AF: 0.0110 AC: 36 AN: 3436

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 03, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.7
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs139705201; hg19: chr9-140513347;