rs723819

Positions:

• chr4-176313795-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000512634.1(SPCS3-AS1):​n.315-2212A>G variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPCS3-AS1	ENST00000512634.1	n.315-2212A>G		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.614

Gnomad4 AMR AF: 0.279

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.614

Gnomad4 SAS AF: 0.446

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.340

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs723819; hg19: chr4-177234946;