10-97686149-G-T

Variant names:

• chr10-97686149-G-T
• rs2151933
• NM_021732.3:c.-11+617C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_021732.3(AVPI1):​c.-11+617C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0411 in 152,200 control chromosomes in the GnomAD database, including 232 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.041 (232 hom., cov: 32)
• Consequence: AVPI1 NM_021732.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22
• Publications: 1 publications found

Genes affected

AVPI1 (HGNC:30898): (arginine vasopressin induced 1) Predicted to act upstream of or within positive regulation of MAPK cascade. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021732.3. 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
	AVPI1	NM_021732.3	MANE Select	c.-11+617C>A		intron	N/A	NP_068378.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AVPI1	ENST00000370626.4	TSL:1 MANE Select	c.-11+617C>A		intron	N/A	ENSP00000359660.3

Frequencies

GnomAD3 genomes AF: 0.0410 AC: 6240 AN: 152082 Hom.: 231 Cov.: 32

Gnomad AFR AF: 0.0405

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0975

Gnomad ASJ AF: 0.0161

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.0365

Gnomad FIN AF: 0.0307

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0242

Gnomad OTH AF: 0.0425

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0411 AC: 6252 AN: 152200 Hom.: 232 Cov.: 32 AF XY: 0.0423 AC XY: 3148 AN XY: 74416

African (AFR) AF: 0.0405 AC: 1684 AN: 41530

American (AMR) AF: 0.0980 AC: 1497 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0161 AC: 56 AN: 3468

East Asian (EAS) AF: 0.145 AC: 751 AN: 5186

South Asian (SAS) AF: 0.0367 AC: 177 AN: 4820

European-Finnish (FIN) AF: 0.0307 AC: 325 AN: 10590

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0242 AC: 1649 AN: 68010

Other (OTH) AF: 0.0416 AC: 88 AN: 2114

Alfa AF: 0.0293 Hom.: 146

Bravo AF: 0.0490

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.4
DANN	Benign	0.77
PhyloP100		1.2
Mutation Taster		=100/0	polymorphism (auto)

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: rs2151933; hg19: chr10-99445906;