rs10707359

Variant names:

• chr3-119295140-CTTTTTTTTT-C
• rs10707359
• NM_020754.4:c.100+140_100+148delTTTTTTTTT

Your query was ambiguous. Multiple possible variants found:

• chr3-119295140-CTTTTTTTTT-C
• chr3-119295140-CTTTTTTTTT-CTTTTTT
• chr3-119295140-CTTTTTTTTT-CTTTTTTT
• chr3-119295140-CTTTTTTTTT-CTTTTTTTT
• chr3-119295140-CTTTTTTTTT-CTTTTTTTTTT
• chr3-119295140-CTTTTTTTTT-CTTTTTTTTTTT

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_020754.4(ARHGAP31):​c.100+140_100+148delTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 484,184 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 17)
  • Exomes 𝑓: 0.0000062 (0 hom.)
• Consequence: ARHGAP31 NM_020754.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770
• Publications: 0 publications found

Genes affected

ARHGAP31 (HGNC:29216): (Rho GTPase activating protein 31) This gene encodes a GTPase-activating protein (GAP). A variety of cellular processes are regulated by Rho GTPases which cycle between an inactive form bound to GDP and an active form bound to GTP. This cycling between inactive and active forms is regulated by guanine nucleotide exchange factors and GAPs. The encoded protein is a GAP shown to regulate two GTPases involved in protein trafficking and cell growth. [provided by RefSeq, Jul 2008]

ARHGAP31 Gene-Disease associations (from GenCC):

• Adams-Oliver syndrome 1

  Inheritance: AD Classification: STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
• Adams-Oliver syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARHGAP31	NM_020754.4	c.100+140_100+148delTTTTTTTTT		intron_variant	Intron 1 of 11	ENST00000264245.9	NP_065805.2
ARHGAP31	XM_006713714.4	c.100+140_100+148delTTTTTTTTT		intron_variant	Intron 1 of 11		XP_006713777.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARHGAP31	ENST00000264245.9	c.100+137_100+145delTTTTTTTTT		intron_variant	Intron 1 of 11	1	NM_020754.4	ENSP00000264245.4

Frequencies

GnomAD3 genomes Cov.: 17

GnomAD4 exome AF: 0.00000620 AC: 3 AN: 484184 Hom.: 0 AF XY: 0.00000772 AC XY: 2 AN XY: 258908

African (AFR) AF: 0.00 AC: 0 AN: 11854

American (AMR) AF: 0.00 AC: 0 AN: 19724

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14826

East Asian (EAS) AF: 0.00 AC: 0 AN: 25316

South Asian (SAS) AF: 0.00 AC: 0 AN: 46716

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 29114

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2906

European-Non Finnish (NFE) AF: 0.00000649 AC: 2 AN: 308364

Other (OTH) AF: 0.0000394 AC: 1 AN: 25364

GnomAD4 genome Cov.: 17

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.077

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10707359; hg19: chr3-119013987;