20-49988570-C-T

Position:

• chr20-49988570-C-T

Variant summary

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

The ENST00000244050.3(SNAI1):​c.*514C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0882 in 152,846 control chromosomes in the GnomAD database, including 700 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 0.088 (696 hom., cov: 32)
  • Exomes 𝑓: 0.076 (4 hom.)
• Consequence: SNAI1 ENST00000244050.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.77

Genes affected

SNAI1 (HGNC:11128): (snail family transcriptional repressor 1) The Drosophila embryonic protein snail is a zinc finger transcriptional repressor which downregulates the expression of ectodermal genes within the mesoderm. The nuclear protein encoded by this gene is structurally similar to the Drosophila snail protein, and is also thought to be critical for mesoderm formation in the developing embryo. At least two variants of a similar processed pseudogene have been found on chromosome 2. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SNAI1	NM_005985.4	c.*514C>T		3_prime_UTR_variant	3/3	ENST00000244050.3	NP_005976.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNAI1	ENST00000244050.3	c.*514C>T		3_prime_UTR_variant	3/3	1	NM_005985.4	ENSP00000244050	P1

Frequencies

GnomAD3 genomes AF: 0.0883 AC: 13421 AN: 152072 Hom.: 693 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.0286

Gnomad AMR AF: 0.0570

Gnomad ASJ AF: 0.0876

Gnomad EAS AF: 0.0354

Gnomad SAS AF: 0.0386

Gnomad FIN AF: 0.0743

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0727

Gnomad OTH AF: 0.0805

GnomAD4 exome AF: 0.0760 AC: 50 AN: 658 Hom.: 4 Cov.: 0 AF XY: 0.0924 AC XY: 34 AN XY: 368

Gnomad4 AFR exome AF: 0.333

Gnomad4 AMR exome AF: 0.0278

Gnomad4 ASJ exome AF: 0.167

Gnomad4 EAS exome AF: 0.0833

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0943

Gnomad4 NFE exome AF: 0.0592

Gnomad4 OTH exome AF: 0.111

GnomAD4 genome AF: 0.0883 AC: 13437 AN: 152188 Hom.: 696 Cov.: 32 AF XY: 0.0868 AC XY: 6461 AN XY: 74414

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.0570

Gnomad4 ASJ AF: 0.0876

Gnomad4 EAS AF: 0.0355

Gnomad4 SAS AF: 0.0391

Gnomad4 FIN AF: 0.0743

Gnomad4 NFE AF: 0.0727

Gnomad4 OTH AF: 0.0796

Alfa AF: 0.0715 Hom.: 610

Bravo AF: 0.0898

Asia WGS AF: 0.0380 AC: 130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	12
DANN	Benign	0.69

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1047920; hg19: chr20-48605107;