rs375614248

Positions:

• chr15-72474873-TGGCGGCGGCGGCGGC-T
• chr15-72474873-TGGCGGCGGCGGCGGC-TGGC
• chr15-72474873-TGGCGGCGGCGGCGGC-TGGCGGC
• chr15-72474873-TGGCGGCGGCGGCGGC-TGGCGGCGGC
• chr15-72474873-TGGCGGCGGCGGCGGC-TGGCGGCGGCGGC
• chr15-72474873-TGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGC
• chr15-72474873-TGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGCGGC
• chr15-72474873-TGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGCGGCGGC
• chr15-72474873-TGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGCGGCGGCGGC
• chr15-72474873-TGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_005744.5(ARIH1):​c.243_257del​(p.Gly86_Gly90del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.00000283 in 1,413,116 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0000067 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0000024 (0 hom.)
• Consequence: ARIH1 NM_005744.5 inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.74

Genes affected

ARIH1 (HGNC:689): (ariadne RBR E3 ubiquitin protein ligase 1) Enables enzyme binding activity; ubiquitin-protein transferase activity; and zinc ion binding activity. Involved in protein ubiquitination. Located in Lewy body; cytoplasm; and nuclear body. Colocalizes with cullin-RING ubiquitin ligase complex. [provided by Alliance of Genome Resources, Apr 2022]

TMEM202-AS1 (HGNC:53265): (TMEM202 antisense RNA 1)

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARIH1	NM_005744.5	c.243_257del	p.Gly86_Gly90del	inframe_deletion	1/14	ENST00000379887.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARIH1	ENST00000379887.9	c.243_257del	p.Gly86_Gly90del	inframe_deletion	1/14	1	NM_005744.5	P1

Frequencies

GnomAD3 genomes AF: 0.00000668 AC: 1 AN: 149696 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000196

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000237 AC: 3 AN: 1263314 Hom.: 0 AF XY: 0.00000484 AC XY: 3 AN XY: 619598

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000171

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.90e-7

Gnomad4 OTH exome AF: 0.0000194

GnomAD4 genome AF: 0.00000668 AC: 1 AN: 149802 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 73150

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000197

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs375614248; hg19: chr15-72767214;