7-150322539-T-C

Variant names:

• chr7-150322539-T-C
• rs2108852
• NM_001164458.2:c.-52+930A>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+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
• Publications: 6 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]

ENSG00000293476 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ACTR3C	NM_001164458.2	c.-52+930A>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+930A>G		intron_variant	Intron 1 of 7		NM_001164458.2	ENSP00000507618.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.600 AC: 6 AN: 10

Other (OTH) AF: 0.500 AC: 1 AN: 2

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

African (AFR) AF: 0.225 AC: 9333 AN: 41452

American (AMR) AF: 0.194 AC: 2959 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1141 AN: 3466

East Asian (EAS) AF: 0.417 AC: 2140 AN: 5136

South Asian (SAS) AF: 0.273 AC: 1319 AN: 4824

European-Finnish (FIN) AF: 0.306 AC: 3226 AN: 10540

Middle Eastern (MID) AF: 0.257 AC: 75 AN: 292

European-Non Finnish (NFE) AF: 0.258 AC: 17521 AN: 67904

Other (OTH) AF: 0.237 AC: 499 AN: 2108

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
PhyloP100		-0.64
PromoterAI		0.13	Neutral
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: rs2108852; hg19: chr7-150019628;