rs557077

Positions:

• chr3-55497239-G-A
• chr3-55497239-G-C

Variant summary

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

The ENST00000472238.1(ENSG00000242317):​n.337+150C>T 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 0.347 in 152,188 control chromosomes in the GnomAD database, including 12,422 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 0.35 (12419 hom., cov: 33)
  • Exomes 𝑓: 0.35 (3 hom.)
• Consequence: ENST00000472238.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.489

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WNT5A	XM_011534086.3	c.-482+150C>T		intron_variant
WNT5A	XM_017007128.2	c.-487+150C>T		intron_variant
WNT5A	XM_047448853.1	c.-3984+150C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000472238.1	n.337+150C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52785 AN: 152044 Hom.: 12405 Cov.: 33

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.313

GnomAD4 exome AF: 0.346 AC: 9 AN: 26 Hom.: 3 AF XY: 0.444 AC XY: 8 AN XY: 18

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.450

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.347 AC: 52835 AN: 152162 Hom.: 12419 Cov.: 33 AF XY: 0.346 AC XY: 25739 AN XY: 74376

Gnomad4 AFR AF: 0.678

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.308

Alfa AF: 0.232 Hom.: 7053

Bravo AF: 0.366

Asia WGS AF: 0.261 AC: 906 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.13
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs557077; hg19: chr3-55531267;