12-18085682-TATAG-T

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_001286201.2(RERGL):c.117_120del(p.Tyr40ArgfsTer11) variant causes a frameshift change. The variant allele was found at a frequency of 0.000664 in 1,595,318 control chromosomes in the GnomAD database, including 8 homozygotes. Variant has been reported in ClinVar as Benign (★). Variant results in nonsense mediated mRNA decay.

• Frequency:
  • Genomes: 𝑓 0.0037 (5 hom., cov: 32)
  • Exomes 𝑓: 0.00034 (3 hom.)
• Consequence: RERGL NM_001286201.2 frameshift
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 6.92

Genes affected

RERGL (HGNC:26213): (RERG like) Predicted to enable G protein activity and GTP binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP6: Variant 12-18085682-TATAG-T is Benign according to our data. Variant chr12-18085682-TATAG-T is described in ClinVar as [Benign]. Clinvar id is 714175.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RERGL	NM_001286201.2	c.117_120del	p.Tyr40ArgfsTer11	frameshift_variant	3/5	ENST00000538724.6
RERGL	NM_024730.4	c.120_123del	p.Tyr41ArgfsTer11	frameshift_variant	4/6
RERGL	NR_104413.1	n.170_173del		non_coding_transcript_exon_variant	3/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RERGL	ENST00000538724.6	c.117_120del	p.Tyr40ArgfsTer11	frameshift_variant	3/5	2	NM_001286201.2	P1

Frequencies

GnomAD3 genomes AF: 0.00371 AC: 564 AN: 152166 Hom.: 5 Cov.: 32

Gnomad AFR AF: 0.0131

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000785

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000588

Gnomad OTH AF: 0.00239

GnomAD3 exomes AF: 0.000830 AC: 203 AN: 244610 Hom.: 1 AF XY: 0.000575 AC XY: 76 AN XY: 132196

Gnomad AFR exome AF: 0.0111

Gnomad AMR exome AF: 0.000521

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000346

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000536

Gnomad OTH exome AF: 0.000338

GnomAD4 exome AF: 0.000344 AC: 496 AN: 1443034 Hom.: 3 AF XY: 0.000292 AC XY: 210 AN XY: 718574

Gnomad4 AFR exome AF: 0.0116

Gnomad4 AMR exome AF: 0.000553

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000711

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000228

Gnomad4 OTH exome AF: 0.000936

GnomAD4 genome AF: 0.00370 AC: 563 AN: 152284 Hom.: 5 Cov.: 32 AF XY: 0.00363 AC XY: 270 AN XY: 74458

Gnomad4 AFR AF: 0.0130

Gnomad4 AMR AF: 0.000784

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000588

Gnomad4 OTH AF: 0.00237

Alfa AF: 0.000418 Hom.: 0

Bravo AF: 0.00399

Asia WGS AF: 0.00144 AC: 5 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Dec 31, 2019

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Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs367672198; hg19: chr12-18238616;