5-91102200-CTTTTT-CTTTT

Variant names:

• chr5-91102200-CT-C
• rs140911567
• NM_032119.4:c.18311-9delT

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_032119.4(ADGRV1):​c.18311-9delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00271 in 1,365,544 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.000013 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0030 (0 hom.)
• Consequence: ADGRV1 NM_032119.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• 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: Likely_benign. The variant received -2 ACMG points.

• BP6: Variant 5-91102200-CT-C is Benign according to our data. Variant chr5-91102200-CT-C is described in ClinVar as Benign. ClinVar VariationId is 2983381.Status of the report is criteria_provided_single_submitter, 1 stars.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADGRV1	NM_032119.4	MANE Select	c.18311-9delT		intron	N/A	NP_115495.3	Q8WXG9-1
	ADGRV1	NR_003149.2		n.18327-9delT		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADGRV1	ENST00000405460.9	TSL:1 MANE Select	c.18311-18delT		intron	N/A	ENSP00000384582.2	Q8WXG9-1
	ADGRV1	ENST00000638510.1	TSL:1	n.5578-18delT		intron	N/A
	ADGRV1	ENST00000425867.3	TSL:5	c.7265-18delT		intron	N/A	ENSP00000392618.3	A0A1X7SBU6

Frequencies

GnomAD3 genomes AF: 0.0000134 AC: 2 AN: 149686 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000245

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000195

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

GnomAD2 exomes AF: 0.00954 AC: 1201 AN: 125934 AF XY: 0.0101

Gnomad AFR exome AF: 0.00610

Gnomad AMR exome AF: 0.0122

Gnomad ASJ exome AF: 0.00751

Gnomad EAS exome AF: 0.00792

Gnomad FIN exome AF: 0.00847

Gnomad NFE exome AF: 0.00934

Gnomad OTH exome AF: 0.0107

GnomAD4 exome AF: 0.00304 AC: 3695 AN: 1215750 Hom.: 0 Cov.: 30 AF XY: 0.00308 AC XY: 1855 AN XY: 603080

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

African (AFR) AF: 0.00366 AC: 101 AN: 27614

American (AMR) AF: 0.00677 AC: 231 AN: 34108

Ashkenazi Jewish (ASJ) AF: 0.00441 AC: 91 AN: 20638

East Asian (EAS) AF: 0.00364 AC: 112 AN: 30736

South Asian (SAS) AF: 0.00453 AC: 306 AN: 67554

European-Finnish (FIN) AF: 0.00543 AC: 233 AN: 42888

Middle Eastern (MID) AF: 0.00280 AC: 14 AN: 5006

European-Non Finnish (NFE) AF: 0.00260 AC: 2437 AN: 937946

Other (OTH) AF: 0.00345 AC: 170 AN: 49260

⚠️ 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 AF: 0.0000134 AC: 2 AN: 149794 Hom.: 0 Cov.: 32 AF XY: 0.0000274 AC XY: 2 AN XY: 73088

African (AFR) AF: 0.0000245 AC: 1 AN: 40876

American (AMR) AF: 0.00 AC: 0 AN: 15028

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3434

East Asian (EAS) AF: 0.000195 AC: 1 AN: 5116

South Asian (SAS) AF: 0.00 AC: 0 AN: 4732

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10144

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67216

Other (OTH) AF: 0.00 AC: 0 AN: 2052

Alfa AF: 0.0179 Hom.: 0

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.077
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs140911567; hg19: chr5-90398017; COSMIC: COSV67982736;