4-85570364-CTCTTTCTTTCTTTCTTTCTTTCTTTCTT-C

Position:

• chr4-85570364-CTCTTTCTTTCTTTCTTTCTTTCTTTCTT-C

Variant summary

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

The NM_001025616.3(ARHGAP24):​c.-20-131_-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 0.67 (34856 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-CTCTTTCTTTCTTTCTTTCTTTCTTTCTT-C is Benign according to our data. Variant chr4-85570364-CTCTTTCTTTCTTTCTTTCTTTCTTTCTT-C is described in ClinVar as [Benign]. Clinvar id is 1253913.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARHGAP24	NM_001025616.3	c.-20-131_-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.-20-131_-20-104del		intron_variant		2	NM_001025616.3	ENSP00000378611	P1
ARHGAP24	ENST00000503995.5	c.-20-131_-20-104del		intron_variant		1		ENSP00000423206
ARHGAP24	ENST00000505856.1	n.75-131_75-104del		intron_variant, non_coding_transcript_variant		2
ARHGAP24	ENST00000506421.5	n.118-131_118-104del		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.667 AC: 93203 AN: 139788 Hom.: 34865 Cov.: 0

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.856

Gnomad NFE AF: 0.848

Gnomad OTH AF: 0.681

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

GnomAD4 genome AF: 0.666 AC: 93183 AN: 139842 Hom.: 34856 Cov.: 0 AF XY: 0.658 AC XY: 44164 AN XY: 67130

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.597

Gnomad4 ASJ AF: 0.814

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.591

Gnomad4 FIN AF: 0.821

Gnomad4 NFE AF: 0.848

Gnomad4 OTH AF: 0.677

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

Jul 24, 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;