7-150108987-C-T

Variant names:

• chr7-150108987-C-T
• rs17173853
• NM_001351028.2:c.23+175766G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001351028.2(ACTR3C):​c.23+175766G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 151,286 control chromosomes in the GnomAD database, including 2,152 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 0.15 (2152 hom., cov: 31)
• Consequence: ACTR3C NM_001351028.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740
• Publications: 2 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]

ENSG00000303171 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACTR3C	NM_001351028.2	c.23+175766G>A		intron_variant	Intron 6 of 9		NP_001337957.1
ACTR3C	NM_001351029.2	c.60+111258G>A		intron_variant	Intron 2 of 3		NP_001337958.1
ACTR3C	NM_001351030.2	c.60+111258G>A		intron_variant	Intron 2 of 3		NP_001337959.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303171	ENST00000792409.1	n.50+6316G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23061 AN: 151168 Hom.: 2146 Cov.: 31

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.0519

Gnomad AMR AF: 0.0905

Gnomad ASJ AF: 0.0887

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.0809

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.153 AC: 23094 AN: 151286 Hom.: 2152 Cov.: 31 AF XY: 0.153 AC XY: 11279 AN XY: 73926

African (AFR) AF: 0.229 AC: 9357 AN: 40858

American (AMR) AF: 0.0902 AC: 1373 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.0887 AC: 308 AN: 3472

East Asian (EAS) AF: 0.125 AC: 648 AN: 5170

South Asian (SAS) AF: 0.0803 AC: 386 AN: 4806

European-Finnish (FIN) AF: 0.214 AC: 2257 AN: 10538

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8428 AN: 67906

Other (OTH) AF: 0.130 AC: 273 AN: 2108

Alfa AF: 0.127 Hom.: 3730

Bravo AF: 0.149

Asia WGS AF: 0.134 AC: 465 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.9
DANN	Benign	0.56
PhyloP100		0.074

Splicing

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

Other links and lift over

dbSNP: rs17173853; hg19: chr7-149806076;