chr3-18880280-T-C

Position:

• chr3-18880280-T-C

Variant summary

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

The variant allele was found at a frequency of 0.33 in 151,914 control chromosomes in the GnomAD database, including 10,175 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 0.33 (10175 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.00

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.18880280T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SATB1-AS1	ENST00000425799.7	n.464-26421T>C		intron_variant		5
SATB1-AS1	ENST00000626982.2	n.352-22224T>C		intron_variant		5
SATB1-AS1	ENST00000630271.2	n.469-26421T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50080 AN: 151794 Hom.: 10151 Cov.: 32

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.330 AC: 50157 AN: 151914 Hom.: 10175 Cov.: 32 AF XY: 0.322 AC XY: 23927 AN XY: 74256

Gnomad4 AFR AF: 0.590

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.285

Alfa AF: 0.247 Hom.: 9948

Bravo AF: 0.349

Asia WGS AF: 0.229 AC: 798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.11
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4973706; hg19: chr3-18921772;