NM_032119.4:c.18803-13A>G

Variant names:

• chr5-91163769-A-G
• rs41305902
• NM_032119.4:c.18803-13A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BP6_Very_Strong

The NM_032119.4(ADGRV1):​c.18803-13A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000759 in 1,246,720 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.00085 (1 hom., cov: 32)
  • Exomes 𝑓: 0.00075 (0 hom.)
• Consequence: ADGRV1 NM_032119.4 intron
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:6
• Conservation: PhyloP100: 0.187
• Publications: 1 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)

LOC107986432 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 5-91163769-A-G is Benign according to our data. Variant chr5-91163769-A-G is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 46303.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 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.18803-13A>G		intron	N/A	NP_115495.3
	ADGRV1	NR_003149.2		n.18819-13A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADGRV1	ENST00000405460.9	TSL:1 MANE Select	c.18803-13A>G		intron	N/A	ENSP00000384582.2
	ADGRV1	ENST00000638510.1	TSL:1	n.6070-13A>G		intron	N/A
	ADGRV1	ENST00000425867.3	TSL:5	c.7757-13A>G		intron	N/A	ENSP00000392618.3

Frequencies

GnomAD3 genomes AF: 0.000848 AC: 129 AN: 152072 Hom.: 1 Cov.: 32

Gnomad AFR AF: 0.000242

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00387

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: 0.000779

Gnomad OTH AF: 0.00335

GnomAD2 exomes AF: 0.000841 AC: 160 AN: 190176 AF XY: 0.000748

Gnomad AFR exome AF: 0.0000858

Gnomad AMR exome AF: 0.00354

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000658

Gnomad OTH exome AF: 0.00191

GnomAD4 exome AF: 0.000746 AC: 817 AN: 1094530 Hom.: 0 Cov.: 14 AF XY: 0.000716 AC XY: 396 AN XY: 552896

African (AFR) AF: 0.0000766 AC: 2 AN: 26102

American (AMR) AF: 0.00326 AC: 120 AN: 36814

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 21352

East Asian (EAS) AF: 0.00 AC: 0 AN: 36752

South Asian (SAS) AF: 0.00 AC: 0 AN: 71472

European-Finnish (FIN) AF: 0.0000197 AC: 1 AN: 50672

Middle Eastern (MID) AF: 0.000200 AC: 1 AN: 4988

European-Non Finnish (NFE) AF: 0.000818 AC: 653 AN: 798634

Other (OTH) AF: 0.000838 AC: 40 AN: 47744

GnomAD4 genome AF: 0.000848 AC: 129 AN: 152190 Hom.: 1 Cov.: 32 AF XY: 0.000874 AC XY: 65 AN XY: 74410

African (AFR) AF: 0.000241 AC: 10 AN: 41516

American (AMR) AF: 0.00386 AC: 59 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.00 AC: 0 AN: 4818

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10602

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000779 AC: 53 AN: 68008

Other (OTH) AF: 0.00331 AC: 7 AN: 2112

Alfa AF: 0.000727 Hom.: 0

Bravo AF: 0.00125

ClinVar

ClinVar submissions as Germline

Significance: Benign/Likely benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	3	not specified (3)
-	-	2	not provided (2)
-	-	1	Usher syndrome type 2C (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.64
PhyloP100		0.19
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: rs41305902; hg19: chr5-90459586;