chr4-85570364-CTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT-C

Position:

• chr4-85570364-CTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT-C

Variant summary

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

The NM_001025616.3(ARHGAP24):​c.-20-139_-20-104del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: 𝑓 0.014 (86 hom., cov: 0)
• Consequence: ARHGAP24 NM_001025616.3 intron
• Clinical Significance: Likely 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-CTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT-C is Benign according to our data. Variant chr4-85570364-CTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT-C is described in ClinVar as [Likely_benign]. Clinvar id is 1706919.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARHGAP24	NM_001025616.3	c.-20-139_-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.-20-139_-20-104del		intron_variant		2	NM_001025616.3	ENSP00000378611	P1
ARHGAP24	ENST00000503995.5	c.-20-139_-20-104del		intron_variant		1		ENSP00000423206
ARHGAP24	ENST00000505856.1	n.75-139_75-104del		intron_variant, non_coding_transcript_variant		2
ARHGAP24	ENST00000506421.5	n.118-139_118-104del		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0139 AC: 1942 AN: 139998 Hom.: 87 Cov.: 0

Gnomad AFR AF: 0.00588

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00976

Gnomad ASJ AF: 0.00912

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.00602

Gnomad FIN AF: 0.0665

Gnomad MID AF: 0.00327

Gnomad NFE AF: 0.00572

Gnomad OTH AF: 0.0163

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

GnomAD4 genome AF: 0.0138 AC: 1938 AN: 140052 Hom.: 86 Cov.: 0 AF XY: 0.0166 AC XY: 1115 AN XY: 67234

Gnomad4 AFR AF: 0.00590

Gnomad4 AMR AF: 0.00975

Gnomad4 ASJ AF: 0.00912

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.00604

Gnomad4 FIN AF: 0.0665

Gnomad4 NFE AF: 0.00570

Gnomad4 OTH AF: 0.0161

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

May 22, 2021

See Variant Classification Assertion Criteria. -

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;