20-149223-C-T

Variant names:

• chr20-149223-C-T
• rs6054706

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 0.536 in 149,064 control chromosomes in the GnomAD database, including 21,806 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 0.54 (21806 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.556 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: 0.536 AC: 79892 AN: 148952 Hom.: 21782 Cov.: 32

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.572

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.536 AC: 79966 AN: 149064 Hom.: 21806 Cov.: 32 AF XY: 0.535 AC XY: 38938 AN XY: 72796

African (AFR) AF: 0.501 AC: 20515 AN: 40968

American (AMR) AF: 0.561 AC: 8360 AN: 14906

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1715 AN: 3400

East Asian (EAS) AF: 0.410 AC: 2052 AN: 5006

South Asian (SAS) AF: 0.509 AC: 2373 AN: 4662

European-Finnish (FIN) AF: 0.562 AC: 5776 AN: 10282

Middle Eastern (MID) AF: 0.560 AC: 159 AN: 284

European-Non Finnish (NFE) AF: 0.561 AC: 37339 AN: 66600

Other (OTH) AF: 0.561 AC: 1159 AN: 2066

Alfa AF: 0.447 Hom.: 1585

Bravo AF: 0.534

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.7
DANN	Benign	0.74
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs6054706; hg19: chr20-129864;