chr5-142330934-G-A

Variant names:

• chr5-142330934-G-A
• rs10463352
• ENST00000510311.6:n.78+5564G>A

Variant summary

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

The ENST00000510311.6(SPRY4-AS1):​n.78+5564G>A variant causes a intron 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 ENST00000510311.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000510311.6. 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
	SPRY4-AS1	NR_120664.1		n.78+5564G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPRY4-AS1	ENST00000510311.6	TSL:4	n.78+5564G>A		intron	N/A
	SPRY4-AS1	ENST00000515288.4	TSL:2	n.194+5564G>A		intron	N/A
	SPRY4-AS1	ENST00000655828.2		n.34+5564G>A		intron	N/A

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

African (AFR) AF: 0.183 AC: 7589 AN: 41442

American (AMR) AF: 0.336 AC: 5133 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 941 AN: 3468

East Asian (EAS) AF: 0.723 AC: 3742 AN: 5178

South Asian (SAS) AF: 0.422 AC: 2030 AN: 4816

European-Finnish (FIN) AF: 0.454 AC: 4781 AN: 10532

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.416 AC: 28255 AN: 67942

Other (OTH) AF: 0.353 AC: 745 AN: 2108

Alfa AF: 0.378 Hom.: 14646

Bravo AF: 0.338

Asia WGS AF: 0.543 AC: 1887 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.26
DANN	Benign	0.42
PhyloP100		-1.4

Splicing

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

Other links and lift over

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