chr5-91102200-C-CTT

Variant names:

• chr5-91102200-C-CTT
• rs140911567
• NM_032119.4:c.18311-10_18311-9dupTT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_032119.4(ADGRV1):​c.18311-10_18311-9dupTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000474 in 1,264,994 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000047 (0 hom.)
• Consequence: ADGRV1 NM_032119.4 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770
• Publications: 0 publications found

Genes affected

ADGRV1 (HGNC:17416): (adhesion G protein-coupled receptor V1) This gene encodes a member of the G-protein coupled receptor superfamily. The encoded protein contains a 7-transmembrane receptor domain, binds calcium and is expressed in the central nervous system. Mutations in this gene are associated with Usher syndrome 2 and familial febrile seizures. Several alternatively spliced transcripts have been described. [provided by RefSeq, Jul 2008]

LUCAT1 (HGNC:48498): (lung cancer associated transcript 1)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032119.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADGRV1	NM_032119.4	MANE Select	c.18311-10_18311-9dupTT		splice_region intron	N/A	NP_115495.3
	ADGRV1	NR_003149.2		n.18327-10_18327-9dupTT		splice_region intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADGRV1	ENST00000405460.9	TSL:1 MANE Select	c.18311-19_18311-18insTT		intron	N/A	ENSP00000384582.2
	ADGRV1	ENST00000638510.1	TSL:1	n.5578-19_5578-18insTT		intron	N/A
	ADGRV1	ENST00000425867.3	TSL:5	c.7265-19_7265-18insTT		intron	N/A	ENSP00000392618.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000474 AC: 6 AN: 1264994 Hom.: 0 Cov.: 30 AF XY: 0.00000159 AC XY: 1 AN XY: 627958

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 28766

American (AMR) AF: 0.00 AC: 0 AN: 35878

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 21736

East Asian (EAS) AF: 0.00 AC: 0 AN: 32578

South Asian (SAS) AF: 0.00 AC: 0 AN: 71418

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 44776

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5156

European-Non Finnish (NFE) AF: 0.00000616 AC: 6 AN: 973260

Other (OTH) AF: 0.00 AC: 0 AN: 51426

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.077

Splicing

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

Other links and lift over

dbSNP: rs140911567; hg19: chr5-90398017;