chr4-176313795-T-C

Variant names:

• chr4-176313795-T-C
• rs723819
• ENST00000512634.1:n.315-2212A>G

Variant summary

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

The ENST00000512634.1(SPCS3-AS1):​n.315-2212A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 152,022 control chromosomes in the GnomAD database, including 12,521 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 0.37 (12521 hom., cov: 32)
• Consequence: SPCS3-AS1 ENST00000512634.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 1 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.607 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.367-2212A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPCS3-AS1	ENST00000512634.1	TSL:2	n.315-2212A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55694 AN: 151904 Hom.: 12486 Cov.: 32

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.295

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.367 AC: 55787 AN: 152022 Hom.: 12521 Cov.: 32 AF XY: 0.367 AC XY: 27261 AN XY: 74318

African (AFR) AF: 0.614 AC: 25414 AN: 41424

American (AMR) AF: 0.279 AC: 4262 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 960 AN: 3472

East Asian (EAS) AF: 0.614 AC: 3174 AN: 5170

South Asian (SAS) AF: 0.446 AC: 2149 AN: 4822

European-Finnish (FIN) AF: 0.214 AC: 2268 AN: 10582

Middle Eastern (MID) AF: 0.290 AC: 84 AN: 290

European-Non Finnish (NFE) AF: 0.244 AC: 16613 AN: 67960

Other (OTH) AF: 0.340 AC: 717 AN: 2110

Alfa AF: 0.308 Hom.: 1362

Bravo AF: 0.380

Asia WGS AF: 0.510 AC: 1772 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.74
PhyloP100		-1.1

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: rs723819;

hg19: chr4-177234946;