Variant 1-230988309-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_022786.3(ARV1):c.175-11T>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 1,577,898 control chromosomes in the GnomAD database, including 92,292 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.34 ( 8842 hom., cov: 32)

Exomes 𝑓: 0.33 ( 83450 hom. )

Consequence

ARV1
NM_022786.3 splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.0009114

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0200

Variant links:

Genes affected

ARV1 (HGNC:29561): (ARV1 homolog, fatty acid homeostasis modulator) this gene encodes a transmembrane protein that contains a conserved zinc ribbon motif at the N- terminus. A similar protein in mouse is thought to function in fatty acid homeostasis. Mutations in this gene are associated with early infantile epileptic encephalopathy 38. [provided by RefSeq, Nov 2016]

ARV1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.61).

BP6

Variant 1-230988309-T-C is Benign according to our data. Variant chr1-230988309-T-C is described in ClinVar as [Benign]. Clinvar id is 1192479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARV1	NM_022786.3 linkuse as main transcript	c.175-11T>C		splice_polypyrimidine_tract_variant, intron_variant		ENST00000310256.7	NP_073623.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARV1	ENST00000310256.7 linkuse as main transcript	c.175-11T>C		splice_polypyrimidine_tract_variant, intron_variant		1	NM_022786.3	ENSP00000312458	P1

Frequencies

GnomAD3 genomes

AF:

0.336

AC:

51021

AN:

151944

Hom.:

8837

Cov.:

show subpopulations

Gnomad AFR

AF:

0.329

Gnomad AMI

AF:

0.508

Gnomad AMR

AF:

0.289

Gnomad ASJ

AF:

0.426

Gnomad EAS

AF:

0.526

Gnomad SAS

AF:

0.500

Gnomad FIN

AF:

0.266

Gnomad MID

AF:

0.567

Gnomad NFE

AF:

0.327

Gnomad OTH

AF:

0.362

GnomAD3 exomes

AF:

0.351

AC:

85074

AN:

242140

Hom.:

16211

AF XY:

0.364

AC XY:

47632

AN XY:

130804

show subpopulations

Gnomad AFR exome

AF:

0.329

Gnomad AMR exome

AF:

0.223

Gnomad ASJ exome

AF:

0.444

Gnomad EAS exome

AF:

0.543

Gnomad SAS exome

AF:

0.501

Gnomad FIN exome

AF:

0.265

Gnomad NFE exome

AF:

0.332

Gnomad OTH exome

AF:

0.352

GnomAD4 exome

AF:

0.335

AC:

477317

AN:

1425836

Hom.:

83450

Cov.:

AF XY:

0.342

AC XY:

242902

AN XY:

710280

show subpopulations

Gnomad4 AFR exome

AF:

0.337

Gnomad4 AMR exome

AF:

0.232

Gnomad4 ASJ exome

AF:

0.439

Gnomad4 EAS exome

AF:

0.463

Gnomad4 SAS exome

AF:

0.501

Gnomad4 FIN exome

AF:

0.263

Gnomad4 NFE exome

AF:

0.320

Gnomad4 OTH exome

AF:

0.360

GnomAD4 genome

AF:

0.336

AC:

51045

AN:

152062

Hom.:

8842

Cov.:

AF XY:

0.337

AC XY:

25047

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.328

Gnomad4 AMR

AF:

0.289

Gnomad4 ASJ

AF:

0.426

Gnomad4 EAS

AF:

0.526

Gnomad4 SAS

AF:

0.501

Gnomad4 FIN

AF:

0.266

Gnomad4 NFE

AF:

0.327

Gnomad4 OTH

AF:

0.361

Alfa

AF:

0.339

Hom.:

1717

Bravo

AF:

0.334

Asia WGS

AF:

0.456

AC:

1575

AN:

3456

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Developmental and epileptic encephalopathy, 38

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.61

CADD

Benign

DANN

Benign

0.83

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00091

dbscSNV1_RF

Benign

0.078

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over