rs621884

Positions:

• chr20-1746317-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 0.316 in 151,960 control chromosomes in the GnomAD database, including 7,696 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 0.32 (7696 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.1746317T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000286288	ENST00000671643.1	n.297-4835A>G		intron_variant
ENSG00000286288	ENST00000702291.1	n.99-4835A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.316 AC: 48011 AN: 151844 Hom.: 7686 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.316 AC: 48035 AN: 151960 Hom.: 7696 Cov.: 32 AF XY: 0.316 AC XY: 23469 AN XY: 74292

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.246

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.293

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.334

Gnomad4 OTH AF: 0.299

Alfa AF: 0.318 Hom.: 1314

Bravo AF: 0.310

Asia WGS AF: 0.296 AC: 1029 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.9
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs621884; hg19: chr20-1726963;