rs552471202

Variant names:

• chr1-236686571-GCGCCCGCCGCCCGC-G
• rs552471202
• NM_001103.4:c.-91_-78delCGCCGCCCGCCGCC

Your query was ambiguous. Multiple possible variants found:

• chr1-236686571-GCGCCCGCCGCCCGC-G
• chr1-236686571-GCGCCCGCCGCCCGC-GCGCCCGC
• chr1-236686571-GCGCCCGCCGCCCGC-GCGCCCGCCGCCCGCCGCCCGC
• chr1-236686571-GCGCCCGCCGCCCGC-GCGCCCGCCGCCCGCCGCCCGCCGCCCGC
• chr1-236686571-GCGCCCGCCGCCCGC-GCGCCCGCCGCCCGCCGCCCGCCGCCCGCCGCCCGC

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001103.4(ACTN2):​c.-91_-78delCGCCGCCCGCCGCC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000602 in 1,162,038 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: 30)
  • Exomes 𝑓: 0.0000060 (0 hom.)
• Consequence: ACTN2 NM_001103.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.94

Genes affected

ACTN2 (HGNC:164): (actinin alpha 2) Alpha actinins belong to the spectrin gene superfamily which represents a diverse group of cytoskeletal proteins, including the alpha and beta spectrins and dystrophins. Alpha actinin is an actin-binding protein with multiple roles in different cell types. In nonmuscle cells, the cytoskeletal isoform is found along microfilament bundles and adherens-type junctions, where it is involved in binding actin to the membrane. In contrast, skeletal, cardiac, and smooth muscle isoforms are localized to the Z-disc and analogous dense bodies, where they help anchor the myofibrillar actin filaments. This gene encodes a muscle-specific, alpha actinin isoform that is expressed in both skeletal and cardiac muscles. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2013]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High AC in GnomAdExome4 at 7 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACTN2	NM_001103.4	c.-91_-78delCGCCGCCCGCCGCC		5_prime_UTR_variant	Exon 1 of 21	ENST00000366578.6	NP_001094.1
ACTN2	NM_001278343.2	c.-91_-78delCGCCGCCCGCCGCC		5_prime_UTR_variant	Exon 1 of 21		NP_001265272.1
ACTN2	NR_184402.1	n.85_98delCGCCGCCCGCCGCC		non_coding_transcript_exon_variant	Exon 1 of 23

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACTN2	ENST00000366578	c.-91_-78delCGCCGCCCGCCGCC		5_prime_UTR_variant	Exon 1 of 21	1	NM_001103.4	ENSP00000355537.4

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome AF: 0.00000602 AC: 7 AN: 1162038 Hom.: 0 AF XY: 0.00000529 AC XY: 3 AN XY: 567240

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.000163

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000313

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 30

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

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: rs552471202; hg19: chr1-236849871;