7-150322539-T-C

Position:

• chr7-150322539-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001164458.2(ACTR3C):​c.-52+930A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 151,920 control chromosomes in the GnomAD database, including 5,062 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.25 (5061 hom., cov: 32)
  • Exomes 𝑓: 0.58 (1 hom.)
• Consequence: ACTR3C NM_001164458.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.638

Genes affected

ACTR3C (HGNC:37282): (actin related protein 3C) Predicted to enable ATP binding activity. Predicted to contribute to actin filament binding activity. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

LRRC61 (HGNC:21704): (leucine rich repeat containing 61) Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACTR3C (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACTR3C	NM_001164458.2	c.-52+930A>G		intron_variant		ENST00000683684.1	NP_001157930.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACTR3C	ENST00000683684.1	c.-52+930A>G		intron_variant			NM_001164458.2	ENSP00000507618.1
ACTR3C	ENST00000478393.5	c.105+930A>G		intron_variant		1		ENSP00000417426.1
ACTR3C	ENST00000477871.1	c.246+930A>G		intron_variant		3		ENSP00000418635.1
ACTR3C	ENST00000477367.1	c.-52+327A>G		intron_variant		4		ENSP00000417997.1

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38554 AN: 151790 Hom.: 5067 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.239

GnomAD4 exome AF: 0.583 AC: 7 AN: 12 Hom.: 1 AF XY: 0.500 AC XY: 4 AN XY: 8

Gnomad4 NFE exome AF: 0.600

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.254 AC: 38562 AN: 151908 Hom.: 5061 Cov.: 32 AF XY: 0.257 AC XY: 19099 AN XY: 74212

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.417

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.258

Gnomad4 OTH AF: 0.237

Alfa AF: 0.254 Hom.: 685

Bravo AF: 0.246

Asia WGS AF: 0.330 AC: 1148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.7
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2108852; hg19: chr7-150019628;