20-5613786-T-G

Variant names:

• chr20-5613786-T-G
• rs6116869

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 0.714 in 152,186 control chromosomes in the GnomAD database, including 40,222 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 0.71 (40222 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.209
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.905 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: 0.714 AC: 108550 AN: 152068 Hom.: 40169 Cov.: 34

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.713

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.703

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

GnomAD4 genome AF: 0.714 AC: 108658 AN: 152186 Hom.: 40222 Cov.: 34 AF XY: 0.707 AC XY: 52617 AN XY: 74390

African (AFR) AF: 0.913 AC: 37921 AN: 41544

American (AMR) AF: 0.664 AC: 10152 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.704 AC: 2445 AN: 3472

East Asian (EAS) AF: 0.730 AC: 3781 AN: 5182

South Asian (SAS) AF: 0.636 AC: 3072 AN: 4828

European-Finnish (FIN) AF: 0.508 AC: 5355 AN: 10546

Middle Eastern (MID) AF: 0.716 AC: 209 AN: 292

European-Non Finnish (NFE) AF: 0.642 AC: 43633 AN: 68008

Other (OTH) AF: 0.707 AC: 1491 AN: 2108

Alfa AF: 0.671 Hom.: 5727

Bravo AF: 0.736

Asia WGS AF: 0.676 AC: 2351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.8
DANN	Benign	0.72
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs6116869; hg19: chr20-5594432;