rs10463352

Positions:

• chr5-142330934-G-A
• chr5-142330934-G-T

Variant summary

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

The NR_120664.1(SPRY4-AS1):​n.78+5564G>A 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 0.353 in 151,956 control chromosomes in the GnomAD database, including 10,601 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 0.35 (10601 hom., cov: 32)
• Consequence: SPRY4-AS1 NR_120664.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

Genes affected

SPRY4-AS1 (HGNC:53465): (SPRY4 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPRY4-AS1	NR_120664.1	n.78+5564G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPRY4-AS1	ENST00000510311.5	n.78+5564G>A		intron_variant, non_coding_transcript_variant		4
SPRY4-AS1	ENST00000515288.3	n.162+5564G>A		intron_variant, non_coding_transcript_variant		2
SPRY4-AS1	ENST00000700840.1	n.156+5564G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53555 AN: 151838 Hom.: 10587 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.353 AC: 53612 AN: 151956 Hom.: 10601 Cov.: 32 AF XY: 0.354 AC XY: 26262 AN XY: 74240

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.336

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.723

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.454

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.353

Alfa AF: 0.386 Hom.: 11537

Bravo AF: 0.338

Asia WGS AF: 0.543 AC: 1887 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.26
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10463352; hg19: chr5-141710499; COSMIC: COSV72545973;