9-125307948-G-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000394084.5(GAPVD1):c.*15G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 1,049,510 control chromosomes in the GnomAD database, including 129,913 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.51 (20105 hom., cov: 32)
  • Exomes 𝑓: 0.49 (109808 hom.)
• Consequence: GAPVD1 ENST00000394084.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.638

Genes affected

GAPVD1 (HGNC:23375): (GTPase activating protein and VPS9 domains 1) Enables GTPase activating protein binding activity and guanyl-nucleotide exchange factor activity. Involved in regulation of protein transport. Located in cytosol and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BP6: Variant 9-125307948-G-C is Benign according to our data. Variant chr9-125307948-G-C is described in ClinVar as [Benign]. Clinvar id is 1230548.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GAPVD1	NM_001282680.3	c.1441+68G>C		intron_variant		ENST00000297933.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAPVD1	ENST00000297933.11	c.1441+68G>C		intron_variant		1	NM_001282680.3	P3

Frequencies

GnomAD3 genomes AF: 0.512 AC: 77827 AN: 151866 Hom.: 20084 Cov.: 32

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.506

GnomAD3 exomes AF: 0.511 AC: 117628 AN: 230180 Hom.: 29935 AF XY: 0.512 AC XY: 64450 AN XY: 125880

Gnomad AFR exome AF: 0.582

Gnomad AMR exome AF: 0.489

Gnomad ASJ exome AF: 0.445

Gnomad EAS exome AF: 0.559

Gnomad SAS exome AF: 0.570

Gnomad FIN exome AF: 0.523

Gnomad NFE exome AF: 0.488

Gnomad OTH exome AF: 0.502

GnomAD4 exome AF: 0.491 AC: 440413 AN: 897526 Hom.: 109808 Cov.: 12 AF XY: 0.494 AC XY: 231848 AN XY: 469156

Gnomad4 AFR exome AF: 0.579

Gnomad4 AMR exome AF: 0.491

Gnomad4 ASJ exome AF: 0.446

Gnomad4 EAS exome AF: 0.547

Gnomad4 SAS exome AF: 0.569

Gnomad4 FIN exome AF: 0.524

Gnomad4 NFE exome AF: 0.473

Gnomad4 OTH exome AF: 0.495

GnomAD4 genome AF: 0.513 AC: 77894 AN: 151984 Hom.: 20105 Cov.: 32 AF XY: 0.514 AC XY: 38171 AN XY: 74270

Gnomad4 AFR AF: 0.572

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.452

Gnomad4 EAS AF: 0.551

Gnomad4 SAS AF: 0.540

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.509

Alfa AF: 0.493 Hom.: 3480

Bravo AF: 0.509

Asia WGS AF: 0.552 AC: 1921 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 11, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.2
Dann	Benign	0.70
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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

Publications

LitVar

Other links and lift over

dbSNP: rs1333055; hg19: chr9-128070227; COSMIC: COSV52920232; COSMIC: COSV52920232;