7-150323292-G-T

Variant names:

• chr7-150323292-G-T
• rs1962004
• ENST00000323078.7:c.-413G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000683684.1(ACTR3C):​c.-52+177C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ACTR3C ENST00000683684.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.46
• Publications: 24 publications found

Genes affected

LRRC61 (HGNC:21704): (leucine rich repeat containing 61) Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

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]

ENSG00000293476 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000683684.1. 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+177C>A		intron	N/A	NP_001157930.1
	LRRC61	NM_001363433.1		c.-315+80G>T		intron	N/A	NP_001350362.1
	LRRC61	NM_001363434.1		c.-314-2549G>T		intron	N/A	NP_001350363.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC61	ENST00000323078.7	TSL:1	c.-413G>T		5_prime_UTR	Exon 1 of 2	ENSP00000339047.6
	ACTR3C	ENST00000683684.1	MANE Select	c.-52+177C>A		intron	N/A	ENSP00000507618.1
	ACTR3C	ENST00000478393.5	TSL:1	c.105+177C>A		intron	N/A	ENSP00000417426.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 106118 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 59156

African (AFR) AF: 0.00 AC: 0 AN: 474

American (AMR) AF: 0.00 AC: 0 AN: 1262

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2100

East Asian (EAS) AF: 0.00 AC: 0 AN: 386

South Asian (SAS) AF: 0.00 AC: 0 AN: 25996

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 7442

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 400

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 62700

Other (OTH) AF: 0.00 AC: 0 AN: 5358

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.8
DANN	Benign	0.70
PhyloP100		2.5
PromoterAI		0.13	Neutral

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1962004; hg19: chr7-150020381;