chr4-176313944-A-G

Variant names:

• chr4-176313944-A-G
• rs723818
• ENST00000512634.1:n.315-2361T>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.315-2361T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 152,104 control chromosomes in the GnomAD database, including 10,190 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 0.34 (10190 hom., cov: 33)
• Consequence: SPCS3-AS1 ENST00000512634.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.678
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.597 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPCS3-AS1	NR_186171.1		n.367-2361T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPCS3-AS1	ENST00000512634.1	TSL:2	n.315-2361T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51586 AN: 151986 Hom.: 10159 Cov.: 33

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.340 AC: 51675 AN: 152104 Hom.: 10190 Cov.: 33 AF XY: 0.340 AC XY: 25282 AN XY: 74370

African (AFR) AF: 0.518 AC: 21498 AN: 41472

American (AMR) AF: 0.270 AC: 4131 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 959 AN: 3466

East Asian (EAS) AF: 0.615 AC: 3178 AN: 5168

South Asian (SAS) AF: 0.445 AC: 2143 AN: 4820

European-Finnish (FIN) AF: 0.214 AC: 2267 AN: 10586

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.244 AC: 16596 AN: 67990

Other (OTH) AF: 0.319 AC: 673 AN: 2110

Alfa AF: 0.298 Hom.: 998

Bravo AF: 0.349

Asia WGS AF: 0.503 AC: 1749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	10
DANN	Benign	0.61
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs723818; hg19: chr4-177235095;