rs3861862

Variant names:

• chr5-142463127-C-G
• rs3861862
• ENST00000414314.2:n.138-843C>G

Variant summary

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

The ENST00000414314.2(SPRY4-AS1):​n.138-843C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,054 control chromosomes in the GnomAD database, including 1,779 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 0.15 (1779 hom., cov: 32)
• Consequence: SPRY4-AS1 ENST00000414314.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.796
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPRY4-AS1	NR_120664.1	n.507-843C>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPRY4-AS1	ENST00000414314.2	n.138-843C>G		intron_variant	Intron 1 of 3	3
SPRY4-AS1	ENST00000425963.1	n.137-843C>G		intron_variant	Intron 1 of 2	3
SPRY4-AS1	ENST00000443800.5	n.154-843C>G		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22069 AN: 151936 Hom.: 1769 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.0727

Gnomad EAS AF: 0.0376

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.0573

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.146 AC: 22128 AN: 152054 Hom.: 1779 Cov.: 32 AF XY: 0.146 AC XY: 10843 AN XY: 74314

African (AFR) AF: 0.195 AC: 8096 AN: 41450

American (AMR) AF: 0.187 AC: 2851 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0727 AC: 252 AN: 3468

East Asian (EAS) AF: 0.0375 AC: 194 AN: 5170

South Asian (SAS) AF: 0.160 AC: 770 AN: 4820

European-Finnish (FIN) AF: 0.150 AC: 1584 AN: 10574

Middle Eastern (MID) AF: 0.0548 AC: 16 AN: 292

European-Non Finnish (NFE) AF: 0.116 AC: 7906 AN: 67974

Other (OTH) AF: 0.125 AC: 264 AN: 2112

Alfa AF: 0.140 Hom.: 204

Bravo AF: 0.150

Asia WGS AF: 0.116 AC: 402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.6
DANN	Benign	0.64
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs3861862; hg19: chr5-141842692;