20-4684616-A-G

Variant names:

• chr20-4684616-A-G
• rs2756271
• ENST00000652447.1:n.87+446T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000652447.1(ENSG00000293214):​n.87+446T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.614 in 152,086 control chromosomes in the GnomAD database, including 28,860 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 0.61 (28860 hom., cov: 32)
• Consequence: ENSG00000293214 ENST00000652447.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.233
• Publications: 10 publications found

Genes affected

ENSG00000293214 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652447.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293214	ENST00000652447.1		n.87+446T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93244 AN: 151968 Hom.: 28813 Cov.: 32

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.614 AC: 93359 AN: 152086 Hom.: 28860 Cov.: 32 AF XY: 0.615 AC XY: 45718 AN XY: 74340

African (AFR) AF: 0.657 AC: 27258 AN: 41460

American (AMR) AF: 0.666 AC: 10193 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1962 AN: 3466

East Asian (EAS) AF: 0.430 AC: 2216 AN: 5152

South Asian (SAS) AF: 0.516 AC: 2486 AN: 4818

European-Finnish (FIN) AF: 0.643 AC: 6799 AN: 10578

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.594 AC: 40406 AN: 67992

Other (OTH) AF: 0.617 AC: 1306 AN: 2116

Alfa AF: 0.599 Hom.: 46509

Bravo AF: 0.619

Asia WGS AF: 0.491 AC: 1709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.55
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs2756271; hg19: chr20-4665262;