rs6022171

Variant names:

• chr20-52934856-T-G
• rs6022171

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 0.249 in 152,102 control chromosomes in the GnomAD database, including 5,805 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 0.25 (5805 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.64
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37812 AN: 151984 Hom.: 5784 Cov.: 32

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.249 AC: 37881 AN: 152102 Hom.: 5805 Cov.: 32 AF XY: 0.253 AC XY: 18804 AN XY: 74358

African (AFR) AF: 0.381 AC: 15796 AN: 41466

American (AMR) AF: 0.196 AC: 2995 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 702 AN: 3470

East Asian (EAS) AF: 0.607 AC: 3135 AN: 5164

South Asian (SAS) AF: 0.399 AC: 1922 AN: 4818

European-Finnish (FIN) AF: 0.146 AC: 1544 AN: 10580

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11146 AN: 67992

Other (OTH) AF: 0.223 AC: 472 AN: 2112

Alfa AF: 0.203 Hom.: 5821

Bravo AF: 0.255

Asia WGS AF: 0.499 AC: 1736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	13
DANN	Benign	0.50
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs6022171; hg19: chr20-51551395;