rs152439

Variant names:

• chr5-142544830-T-C
• rs152439
• ENST00000414314.2:n.228-36972T>C

Variant summary

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

The ENST00000414314.2(SPRY4-AS1):​n.228-36972T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 151,798 control chromosomes in the GnomAD database, including 8,729 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 0.23 (8729 hom., cov: 32)
• Consequence: SPRY4-AS1 ENST00000414314.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 7 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.62 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPRY4-AS1	ENST00000414314.2	TSL:3	n.228-36972T>C		intron	N/A
	SPRY4-AS1	ENST00000443800.5	TSL:3	n.244-36972T>C		intron	N/A
	SPRY4-AS1	ENST00000510311.6	TSL:4	n.597-36972T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35063 AN: 151682 Hom.: 8704 Cov.: 32

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.0418

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.0467

Gnomad EAS AF: 0.0701

Gnomad SAS AF: 0.0964

Gnomad FIN AF: 0.0838

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.0739

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.231 AC: 35133 AN: 151798 Hom.: 8729 Cov.: 32 AF XY: 0.225 AC XY: 16710 AN XY: 74204

African (AFR) AF: 0.627 AC: 25932 AN: 41378

American (AMR) AF: 0.122 AC: 1856 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.0467 AC: 162 AN: 3466

East Asian (EAS) AF: 0.0703 AC: 360 AN: 5122

South Asian (SAS) AF: 0.0957 AC: 459 AN: 4798

European-Finnish (FIN) AF: 0.0838 AC: 884 AN: 10544

Middle Eastern (MID) AF: 0.147 AC: 43 AN: 292

European-Non Finnish (NFE) AF: 0.0739 AC: 5020 AN: 67926

Other (OTH) AF: 0.179 AC: 379 AN: 2112

Alfa AF: 0.119 Hom.: 4950

Bravo AF: 0.250

Asia WGS AF: 0.132 AC: 460 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.026
DANN	Benign	0.27
PhyloP100		-1.6

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs152439;

hg19: chr5-141924395;