4-176313755-A-G

Variant names:

• chr4-176313755-A-G
• rs723820
• ENST00000512634.1:n.315-2172T>C

Variant summary

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

The ENST00000512634.1(SPCS3-AS1):​n.315-2172T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 152,098 control chromosomes in the GnomAD database, including 6,642 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 (6642 hom., cov: 33)
• Consequence: SPCS3-AS1 ENST00000512634.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.21
• Publications: 2 publications found

Genes affected

SPCS3-AS1 (HGNC:54818): (SPCS3 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000512634.1. 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
	SPCS3-AS1	NR_186171.1		n.367-2172T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPCS3-AS1	ENST00000512634.1	TSL:2	n.315-2172T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42891 AN: 151980 Hom.: 6629 Cov.: 33

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.282 AC: 42944 AN: 152098 Hom.: 6642 Cov.: 33 AF XY: 0.284 AC XY: 21126 AN XY: 74362

African (AFR) AF: 0.321 AC: 13324 AN: 41482

American (AMR) AF: 0.246 AC: 3754 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 958 AN: 3468

East Asian (EAS) AF: 0.614 AC: 3173 AN: 5166

South Asian (SAS) AF: 0.444 AC: 2144 AN: 4826

European-Finnish (FIN) AF: 0.214 AC: 2265 AN: 10574

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16525 AN: 67980

Other (OTH) AF: 0.275 AC: 581 AN: 2110

Alfa AF: 0.263 Hom.: 22420

Bravo AF: 0.284

Asia WGS AF: 0.492 AC: 1709 AN: 3478

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	0.81
PhyloP100		1.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs723820;

hg19: chr4-177234906;