rs2159236

chr7-150320125-A-G

Variant summary

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

The NM_001164458.2(ACTR3C):c.-52+3344T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 152,110 control chromosomes in the GnomAD database, including 4,555 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 0.23 (4555 hom., cov: 33)
• Consequence: ACTR3C NM_001164458.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.328

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:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACTR3C	NM_001164458.2	c.-52+3344T>C		intron_variant		ENST00000683684.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACTR3C	ENST00000683684.1	c.-52+3344T>C		intron_variant			NM_001164458.2	P1
ACTR3C	ENST00000478393.5	c.105+3344T>C		intron_variant		1
ACTR3C	ENST00000477367.1	c.-52+2741T>C		intron_variant		4
ACTR3C	ENST00000477871.1	c.246+3344T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35588 AN: 151992 Hom.: 4563 Cov.: 33

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.234 AC: 35589 AN: 152110 Hom.: 4555 Cov.: 33 AF XY: 0.239 AC XY: 17752 AN XY: 74370

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.328

Gnomad4 EAS AF: 0.417

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.258

Gnomad4 OTH AF: 0.218

Alfa AF: 0.250 Hom.: 587

Bravo AF: 0.221

Asia WGS AF: 0.326 AC: 1134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	5.6
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2159236; hg19: chr7-150017214;