chr5-142434380-A-G

Variant names:

• chr5-142434380-A-G
• rs153423
• ENST00000414314.2:n.138-29590A>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.138-29590A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 152,126 control chromosomes in the GnomAD database, including 6,225 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 0.26 (6225 hom., cov: 33)
• Consequence: SPRY4-AS1 ENST00000414314.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 8 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000414314.2. 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.507-29590A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPRY4-AS1	ENST00000414314.2	TSL:3	n.138-29590A>G		intron	N/A
	SPRY4-AS1	ENST00000425963.1	TSL:3	n.137-29590A>G		intron	N/A
	SPRY4-AS1	ENST00000443800.5	TSL:3	n.154-29590A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39217 AN: 152006 Hom.: 6209 Cov.: 33

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.258 AC: 39280 AN: 152126 Hom.: 6225 Cov.: 33 AF XY: 0.263 AC XY: 19569 AN XY: 74384

African (AFR) AF: 0.377 AC: 15630 AN: 41478

American (AMR) AF: 0.213 AC: 3254 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 689 AN: 3470

East Asian (EAS) AF: 0.680 AC: 3515 AN: 5166

South Asian (SAS) AF: 0.342 AC: 1651 AN: 4822

European-Finnish (FIN) AF: 0.202 AC: 2142 AN: 10600

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11679 AN: 67986

Other (OTH) AF: 0.222 AC: 468 AN: 2108

Alfa AF: 0.204 Hom.: 10932

Bravo AF: 0.264

Asia WGS AF: 0.482 AC: 1673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.7
DANN	Benign	0.72
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs153423; hg19: chr5-141813945;