5-142548268-C-A

Variant names:

• chr5-142548268-C-A
• rs33957
• ENST00000414314.2:n.228-33534C>A

Variant summary

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

The ENST00000414314.2(SPRY4-AS1):​n.228-33534C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 151,736 control chromosomes in the GnomAD database, including 17,592 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 0.41 (17592 hom., cov: 32)
• Consequence: SPRY4-AS1 ENST00000414314.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238
• Publications: 1 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 (AFR) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPRY4-AS1	ENST00000414314.2	n.228-33534C>A		intron_variant	Intron 2 of 3	3
SPRY4-AS1	ENST00000443800.5	n.244-33534C>A		intron_variant	Intron 2 of 3	3
SPRY4-AS1	ENST00000510311.6	n.597-33534C>A		intron_variant	Intron 4 of 7	4

Frequencies

GnomAD3 genomes AF: 0.409 AC: 61951 AN: 151622 Hom.: 17554 Cov.: 32

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.409 AC: 62044 AN: 151736 Hom.: 17592 Cov.: 32 AF XY: 0.408 AC XY: 30220 AN XY: 74088

African (AFR) AF: 0.804 AC: 33321 AN: 41428

American (AMR) AF: 0.246 AC: 3751 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 843 AN: 3462

East Asian (EAS) AF: 0.542 AC: 2792 AN: 5154

South Asian (SAS) AF: 0.391 AC: 1876 AN: 4800

European-Finnish (FIN) AF: 0.260 AC: 2710 AN: 10418

Middle Eastern (MID) AF: 0.293 AC: 85 AN: 290

European-Non Finnish (NFE) AF: 0.233 AC: 15811 AN: 67920

Other (OTH) AF: 0.338 AC: 712 AN: 2108

Alfa AF: 0.199 Hom.: 537

Bravo AF: 0.422

Asia WGS AF: 0.477 AC: 1657 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.51
DANN	Benign	0.53
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs33957; hg19: chr5-141927833;