5-142458169-T-G

Position:

• chr5-142458169-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_120664.1(SPRY4-AS1):​n.507-5801T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0815 in 152,290 control chromosomes in the GnomAD database, including 1,064 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 0.082 (1064 hom., cov: 33)
• Consequence: SPRY4-AS1 NR_120664.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.150

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPRY4-AS1	NR_120664.1	n.507-5801T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPRY4-AS1	ENST00000443800.5	n.154-5801T>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0814 AC: 12389 AN: 152172 Hom.: 1065 Cov.: 33

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0514

Gnomad ASJ AF: 0.00950

Gnomad EAS AF: 0.0250

Gnomad SAS AF: 0.0555

Gnomad FIN AF: 0.0274

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0218

Gnomad OTH AF: 0.0645

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

GnomAD4 genome AF: 0.0815 AC: 12413 AN: 152290 Hom.: 1064 Cov.: 33 AF XY: 0.0801 AC XY: 5970 AN XY: 74486

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.0512

Gnomad4 ASJ AF: 0.00950

Gnomad4 EAS AF: 0.0249

Gnomad4 SAS AF: 0.0553

Gnomad4 FIN AF: 0.0274

Gnomad4 NFE AF: 0.0218

Gnomad4 OTH AF: 0.0638

Alfa AF: 0.0531 Hom.: 76

Bravo AF: 0.0883

Asia WGS AF: 0.0450 AC: 155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.6
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6879787; hg19: chr5-141837734;