5-142540530-C-T

Variant names:

• chr5-142540530-C-T
• rs152442
• ENST00000414314.2:n.228-41272C>T

Variant summary

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

The ENST00000414314.2(SPRY4-AS1):​n.228-41272C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 151,850 control chromosomes in the GnomAD database, including 5,571 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 0.21 (5571 hom., cov: 31)
• Consequence: SPRY4-AS1 ENST00000414314.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106
• 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.494 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.228-41272C>T		intron	N/A
	SPRY4-AS1	ENST00000443800.5	TSL:3	n.244-41272C>T		intron	N/A
	SPRY4-AS1	ENST00000510311.6	TSL:4	n.597-41272C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31714 AN: 151728 Hom.: 5559 Cov.: 31

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.0875

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0800

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.209 AC: 31763 AN: 151850 Hom.: 5571 Cov.: 31 AF XY: 0.210 AC XY: 15612 AN XY: 74220

African (AFR) AF: 0.455 AC: 18795 AN: 41336

American (AMR) AF: 0.128 AC: 1951 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 365 AN: 3470

East Asian (EAS) AF: 0.510 AC: 2625 AN: 5148

South Asian (SAS) AF: 0.252 AC: 1209 AN: 4792

European-Finnish (FIN) AF: 0.0875 AC: 924 AN: 10558

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0799 AC: 5434 AN: 67970

Other (OTH) AF: 0.179 AC: 376 AN: 2104

Alfa AF: 0.112 Hom.: 2795

Bravo AF: 0.222

Asia WGS AF: 0.379 AC: 1318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	10
DANN	Benign	0.77
PhyloP100		-0.11

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: rs152442;

hg19: chr5-141920095;