chr22-19996754-C-T

Variant names:

• chr22-19996754-C-T
• rs1034566
• NM_001670.3:c.-18-5942G>A

Variant summary

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

The NM_001670.3(ARVCF):​c.-18-5942G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 152,140 control chromosomes in the GnomAD database, including 4,594 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 0.23 (4594 hom., cov: 33)
• Consequence: ARVCF NM_001670.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970
• Publications: 26 publications found

Genes affected

ARVCF (HGNC:728): (ARVCF delta catenin family member) Armadillo Repeat gene deleted in Velo-Cardio-Facial syndrome (ARVCF) is a member of the catenin family. This family plays an important role in the formation of adherens junction complexes, which are thought to facilitate communication between the inside and outside environments of a cell. The ARVCF gene was isolated in the search for the genetic defect responsible for the autosomal dominant Velo-Cardio-Facial syndrome (VCFS), a relatively common human disorder with phenotypic features including cleft palate, conotruncal heart defects and facial dysmorphology. The ARVCF gene encodes a protein containing two motifs, a coiled coil domain in the N-terminus and a 10 armadillo repeat sequence in the midregion. Since these sequences can facilitate protein-protein interactions ARVCF is thought to function in a protein complex. In addition, ARVCF contains a predicted nuclear-targeting sequence suggesting that it may have a function as a nuclear protein. [provided by RefSeq, Jun 2010]

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 (SAS) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARVCF	NM_001670.3	c.-18-5942G>A		intron_variant	Intron 2 of 19	ENST00000263207.8	NP_001661.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARVCF	ENST00000263207.8	c.-18-5942G>A		intron_variant	Intron 2 of 19	1	NM_001670.3	ENSP00000263207.3
ARVCF	ENST00000467828.1	n.158-14663G>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34750 AN: 152022 Hom.: 4593 Cov.: 33

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.0706

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.228 AC: 34749 AN: 152140 Hom.: 4594 Cov.: 33 AF XY: 0.230 AC XY: 17065 AN XY: 74354

African (AFR) AF: 0.106 AC: 4406 AN: 41538

American (AMR) AF: 0.223 AC: 3410 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 884 AN: 3468

East Asian (EAS) AF: 0.0705 AC: 365 AN: 5174

South Asian (SAS) AF: 0.327 AC: 1571 AN: 4806

European-Finnish (FIN) AF: 0.330 AC: 3492 AN: 10568

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19604 AN: 67976

Other (OTH) AF: 0.238 AC: 502 AN: 2108

Alfa AF: 0.259 Hom.: 8971

Bravo AF: 0.210

Asia WGS AF: 0.183 AC: 635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.78
DANN	Benign	0.55
PhyloP100		-0.097
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs1034566; hg19: chr22-19984277;