chr7-150312590-A-G

Variant names:

• chr7-150312590-A-G
• rs17837498
• NM_001164458.2:c.-52+10879T>C

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+10879T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 152,024 control chromosomes in the GnomAD database, including 5,934 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 0.28 (5934 hom., cov: 32)
• Consequence: ACTR3C NM_001164458.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.216
• Publications: 10 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001164458.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACTR3C	NM_001164458.2	MANE Select	c.-52+10879T>C		intron	N/A	NP_001157930.1
	LRRC61	NM_001363434.1		c.-315+2690A>G		intron	N/A	NP_001350363.1
	ACTR3C	NM_001351028.2		c.-593+10879T>C		intron	N/A	NP_001337957.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACTR3C	ENST00000683684.1	MANE Select	c.-52+10879T>C		intron	N/A	ENSP00000507618.1
	ACTR3C	ENST00000478393.5	TSL:1	c.105+10879T>C		intron	N/A	ENSP00000417426.1
	ACTR3C	ENST00000477871.1	TSL:3	c.246+10879T>C		intron	N/A	ENSP00000418635.1

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41865 AN: 151906 Hom.: 5943 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.275 AC: 41876 AN: 152024 Hom.: 5934 Cov.: 32 AF XY: 0.278 AC XY: 20688 AN XY: 74330

African (AFR) AF: 0.272 AC: 11268 AN: 41472

American (AMR) AF: 0.207 AC: 3168 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1125 AN: 3468

East Asian (EAS) AF: 0.432 AC: 2225 AN: 5156

South Asian (SAS) AF: 0.290 AC: 1392 AN: 4806

European-Finnish (FIN) AF: 0.312 AC: 3286 AN: 10548

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.271 AC: 18424 AN: 67968

Other (OTH) AF: 0.262 AC: 553 AN: 2112

Alfa AF: 0.271 Hom.: 1272

Bravo AF: 0.269

Asia WGS AF: 0.344 AC: 1198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.44
PhyloP100		0.22
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: rs17837498; hg19: chr7-150009679;