4-85570364-CTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT-C

Position:

• chr4-85570364-CTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001025616.3(ARHGAP24):​c.-20-135_-20-104del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.28 (7868 hom., cov: 0)
• Consequence: ARHGAP24 NM_001025616.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.58

Genes affected

ARHGAP24 (HGNC:25361): (Rho GTPase activating protein 24) This gene encodes a Rho-GTPase activating protein, which is specific for the small GTPase family member Rac. Binding of the encoded protein by filamin A targets it to sites of membrane protrusion, where it antognizes Rac. This results in suppression of lamellae formation and promotion of retraction to regulate cell polarity. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2016]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 4-85570364-CTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT-C is Benign according to our data. Variant chr4-85570364-CTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT-C is described in ClinVar as [Benign]. Clinvar id is 1270853.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARHGAP24	NM_001025616.3	c.-20-135_-20-104del		intron_variant		ENST00000395184.6	NP_001020787.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARHGAP24	ENST00000395184.6	c.-20-135_-20-104del		intron_variant		2	NM_001025616.3	ENSP00000378611	P1
ARHGAP24	ENST00000503995.5	c.-20-135_-20-104del		intron_variant		1		ENSP00000423206
ARHGAP24	ENST00000505856.1	n.75-135_75-104del		intron_variant, non_coding_transcript_variant		2
ARHGAP24	ENST00000506421.5	n.118-135_118-104del		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.279 AC: 39040 AN: 139838 Hom.: 7836 Cov.: 0

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.648

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.280 AC: 39107 AN: 139892 Hom.: 7868 Cov.: 0 AF XY: 0.286 AC XY: 19236 AN XY: 67152

Gnomad4 AFR AF: 0.482

Gnomad4 AMR AF: 0.372

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.649

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.267

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

Jun 18, 2020

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs56272553; hg19: chr4-86491517;