rs621884

Variant names:

• chr20-1746317-T-C
• rs621884
• ENST00000671643.1:n.297-4835A>G

Variant summary

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

The ENST00000671643.1(ENSG00000286288):​n.297-4835A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000286288 ENST00000671643.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118

Genes affected

ENSG00000286288 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286288	ENST00000671643.1	n.297-4835A>G		intron_variant	Intron 1 of 2
ENSG00000286288	ENST00000702291.1	n.99-4835A>G		intron_variant	Intron 1 of 2

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;