20-4720565-G-T

Variant names:

• chr20-4720565-G-T
• rs2326510

Variant summary

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

The variant allele was found at a frequency of 0.366 in 151,972 control chromosomes in the GnomAD database, including 12,718 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 0.37 (12718 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.645 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

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55455 AN: 151854 Hom.: 12673 Cov.: 32

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.0820

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.366 AC: 55568 AN: 151972 Hom.: 12718 Cov.: 32 AF XY: 0.365 AC XY: 27134 AN XY: 74290

African (AFR) AF: 0.651 AC: 26972 AN: 41408

American (AMR) AF: 0.343 AC: 5245 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1228 AN: 3468

East Asian (EAS) AF: 0.0824 AC: 426 AN: 5170

South Asian (SAS) AF: 0.262 AC: 1258 AN: 4806

European-Finnish (FIN) AF: 0.284 AC: 2998 AN: 10562

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.241 AC: 16377 AN: 67968

Other (OTH) AF: 0.328 AC: 694 AN: 2114

Alfa AF: 0.280 Hom.: 26673

Bravo AF: 0.381

Asia WGS AF: 0.191 AC: 667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.12
DANN	Benign	0.35
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs2326510; hg19: chr20-4701211;