ENST00000432677.2:n.158+1469C>G

Variant names:

• chr5-142747191-C-G
• rs1917028
• ENST00000432677.2:n.158+1469C>G

Variant summary

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

The ENST00000432677.2(SPRY4-AS1):​n.158+1469C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 152,128 control chromosomes in the GnomAD database, including 15,837 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 0.33 (15837 hom., cov: 32)
• Consequence: SPRY4-AS1 ENST00000432677.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 2 publications found

Genes affected

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

LINC01844 (HGNC:52660): (long intergenic non-protein coding RNA 1844)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01844	NR_110558.1	n.119+1473C>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPRY4-AS1	ENST00000432677.2	n.158+1469C>G		intron_variant	Intron 1 of 3	1
SPRY4-AS1	ENST00000652722.1	n.136+1469C>G		intron_variant	Intron 1 of 4
SPRY4-AS1	ENST00000652991.1	n.170+1469C>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.329 AC: 50028 AN: 152010 Hom.: 15779 Cov.: 32

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.0880

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.330 AC: 50137 AN: 152128 Hom.: 15837 Cov.: 32 AF XY: 0.330 AC XY: 24505 AN XY: 74354

African (AFR) AF: 0.823 AC: 34138 AN: 41498

American (AMR) AF: 0.282 AC: 4313 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 486 AN: 3466

East Asian (EAS) AF: 0.372 AC: 1925 AN: 5174

South Asian (SAS) AF: 0.280 AC: 1350 AN: 4826

European-Finnish (FIN) AF: 0.113 AC: 1199 AN: 10572

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.0880 AC: 5981 AN: 67996

Other (OTH) AF: 0.296 AC: 625 AN: 2114

Alfa AF: 0.216 Hom.: 1154

Bravo AF: 0.366

Asia WGS AF: 0.374 AC: 1302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.0
DANN	Benign	0.72
PhyloP100		0.30
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs1917028; hg19: chr5-142126756;