NM_001164458.2:c.-52+3150A>G

Variant names:

• chr7-150320319-T-C
• rs2108854
• NM_001164458.2:c.-52+3150A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001164458.2(ACTR3C):​c.-52+3150A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,202 control chromosomes in the GnomAD database, including 5,158 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 (5158 hom., cov: 33)
• Consequence: ACTR3C NM_001164458.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.291
• Publications: 22 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACTR3C	NM_001164458.2	c.-52+3150A>G		intron_variant	Intron 1 of 7	ENST00000683684.1	NP_001157930.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACTR3C	ENST00000683684.1	c.-52+3150A>G		intron_variant	Intron 1 of 7		NM_001164458.2	ENSP00000507618.1
ACTR3C	ENST00000478393.5	c.105+3150A>G		intron_variant	Intron 1 of 5	1		ENSP00000417426.1
ACTR3C	ENST00000477871.1	c.246+3150A>G		intron_variant	Intron 1 of 4	3		ENSP00000418635.1
ACTR3C	ENST00000477367.1	c.-52+2547A>G		intron_variant	Intron 1 of 2	4		ENSP00000417997.1

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38753 AN: 152084 Hom.: 5164 Cov.: 33

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.255 AC: 38761 AN: 152202 Hom.: 5158 Cov.: 33 AF XY: 0.258 AC XY: 19233 AN XY: 74412

African (AFR) AF: 0.226 AC: 9375 AN: 41530

American (AMR) AF: 0.194 AC: 2973 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1134 AN: 3468

East Asian (EAS) AF: 0.418 AC: 2167 AN: 5180

South Asian (SAS) AF: 0.275 AC: 1327 AN: 4824

European-Finnish (FIN) AF: 0.309 AC: 3263 AN: 10574

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17588 AN: 68008

Other (OTH) AF: 0.238 AC: 503 AN: 2116

Alfa AF: 0.260 Hom.: 20245

Bravo AF: 0.246

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.1
DANN	Benign	0.32
PhyloP100		0.29
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2108854; hg19: chr7-150017408;