7-150316906-A-T

Variant names:

• chr7-150316906-A-T
• rs7788316
• NM_001164458.2:c.-52+6563T>A

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+6563T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 151,940 control chromosomes in the GnomAD database, including 6,860 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 (6860 hom., cov: 32)
• Consequence: ACTR3C NM_001164458.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• Publications: 5 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=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.403 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+6563T>A		intron	N/A	NP_001157930.1
	LRRC61	NM_001363434.1		c.-315+7006A>T		intron	N/A	NP_001350363.1
	ACTR3C	NM_001351028.2		c.-593+6563T>A		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+6563T>A		intron	N/A	ENSP00000507618.1
	ACTR3C	ENST00000478393.5	TSL:1	c.105+6563T>A		intron	N/A	ENSP00000417426.1
	ACTR3C	ENST00000477871.1	TSL:3	c.246+6563T>A		intron	N/A	ENSP00000418635.1

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44776 AN: 151822 Hom.: 6855 Cov.: 32

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.295 AC: 44819 AN: 151940 Hom.: 6860 Cov.: 32 AF XY: 0.296 AC XY: 22007 AN XY: 74294

African (AFR) AF: 0.349 AC: 14460 AN: 41406

American (AMR) AF: 0.213 AC: 3249 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1125 AN: 3470

East Asian (EAS) AF: 0.417 AC: 2161 AN: 5180

South Asian (SAS) AF: 0.277 AC: 1335 AN: 4824

European-Finnish (FIN) AF: 0.311 AC: 3272 AN: 10530

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18206 AN: 67952

Other (OTH) AF: 0.271 AC: 573 AN: 2112

Alfa AF: 0.291 Hom.: 793

Bravo AF: 0.292

Asia WGS AF: 0.343 AC: 1194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.21
DANN	Benign	0.30
PhyloP100		-1.7
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: rs7788316; hg19: chr7-150013995;