chr20-1746317-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

ENSG00000286288 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000671643.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286288	ENST00000671643.1		n.297-4835A>G		intron	N/A
	ENSG00000286288	ENST00000702291.2		n.122-4835A>G		intron	N/A
	ENSG00000286288	ENST00000844949.1		n.432-4835A>G		intron	N/A

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

African (AFR) AF: 0.302 AC: 12512 AN: 41450

American (AMR) AF: 0.246 AC: 3764 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1076 AN: 3468

East Asian (EAS) AF: 0.293 AC: 1511 AN: 5156

South Asian (SAS) AF: 0.381 AC: 1831 AN: 4810

European-Finnish (FIN) AF: 0.334 AC: 3521 AN: 10538

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.334 AC: 22682 AN: 67934

Other (OTH) AF: 0.299 AC: 633 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.9
DANN	Benign	0.80
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs621884; hg19: chr20-1726963;