chr7-150311769-T-C

Position:

• chr7-150311769-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+11700A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 152,134 control chromosomes in the GnomAD database, including 6,552 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 0.29 (6552 hom., cov: 32)
• Consequence: ACTR3C NM_001164458.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACTR3C	NM_001164458.2	c.-52+11700A>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+11700A>G		intron_variant			NM_001164458.2	ENSP00000507618.1
ACTR3C	ENST00000478393.5	c.105+11700A>G		intron_variant		1		ENSP00000417426.1
ACTR3C	ENST00000477871.1	c.246+11700A>G		intron_variant		3		ENSP00000418635.1
ACTR3C	ENST00000477367.1	c.-52+11097A>G		intron_variant		4		ENSP00000417997.1

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43909 AN: 152016 Hom.: 6545 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.436

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.289 AC: 43950 AN: 152134 Hom.: 6552 Cov.: 32 AF XY: 0.290 AC XY: 21593 AN XY: 74358

Gnomad4 AFR AF: 0.320

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.435

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.273

Alfa AF: 0.118 Hom.: 204

Bravo AF: 0.284

Asia WGS AF: 0.350 AC: 1219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7781827; hg19: chr7-150008858;