rs11975886

Variant names:

• chr7-150313273-G-A
• rs11975886
• NM_001164458.2:c.-52+10196C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-150313273-G-A
• chr7-150313273-G-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+10196C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 152,054 control chromosomes in the GnomAD database, including 5,943 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 (5943 hom., cov: 32)
• Consequence: ACTR3C NM_001164458.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.227
• Publications: 4 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=-0.75).
• 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACTR3C	NM_001164458.2	MANE Select	c.-52+10196C>T		intron	N/A	NP_001157930.1	Q9C0K3-1
	LRRC61	NM_001363434.1		c.-315+3373G>A		intron	N/A	NP_001350363.1	Q9BV99
	ACTR3C	NM_001351028.2		c.-593+10196C>T		intron	N/A	NP_001337957.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACTR3C	ENST00000683684.1	MANE Select	c.-52+10196C>T		intron	N/A	ENSP00000507618.1	Q9C0K3-1
	ACTR3C	ENST00000478393.5	TSL:1	c.105+10196C>T		intron	N/A	ENSP00000417426.1	H7C4J1
	ACTR3C	ENST00000477871.1	TSL:3	c.246+10196C>T		intron	N/A	ENSP00000418635.1	C9IZN3

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41881 AN: 151936 Hom.: 5952 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: 0.433

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.276 AC: 41892 AN: 152054 Hom.: 5943 Cov.: 32 AF XY: 0.278 AC XY: 20697 AN XY: 74336

African (AFR) AF: 0.272 AC: 11277 AN: 41468

American (AMR) AF: 0.207 AC: 3159 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1124 AN: 3470

East Asian (EAS) AF: 0.432 AC: 2236 AN: 5174

South Asian (SAS) AF: 0.290 AC: 1392 AN: 4808

European-Finnish (FIN) AF: 0.312 AC: 3294 AN: 10560

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18425 AN: 67986

Other (OTH) AF: 0.261 AC: 552 AN: 2112

Alfa AF: 0.283 Hom.: 866

Bravo AF: 0.269

Asia WGS AF: 0.344 AC: 1197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	3.7
DANN	Benign	0.85
PhyloP100		0.23
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: rs11975886; hg19: chr7-150010362;