20-55869369-G-A

Variant names:

• chr20-55869369-G-A
• rs6069437

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 0.441 in 151,884 control chromosomes in the GnomAD database, including 17,034 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 0.44 (17034 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.549 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.441 AC: 66945 AN: 151766 Hom.: 17025 Cov.: 31

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.441 AC: 66960 AN: 151884 Hom.: 17034 Cov.: 31 AF XY: 0.443 AC XY: 32881 AN XY: 74216

African (AFR) AF: 0.172 AC: 7104 AN: 41406

American (AMR) AF: 0.559 AC: 8536 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1823 AN: 3470

East Asian (EAS) AF: 0.414 AC: 2136 AN: 5158

South Asian (SAS) AF: 0.443 AC: 2130 AN: 4804

European-Finnish (FIN) AF: 0.591 AC: 6218 AN: 10528

Middle Eastern (MID) AF: 0.445 AC: 130 AN: 292

European-Non Finnish (NFE) AF: 0.552 AC: 37505 AN: 67926

Other (OTH) AF: 0.454 AC: 960 AN: 2114

Alfa AF: 0.518 Hom.: 89905

Bravo AF: 0.430

Asia WGS AF: 0.366 AC: 1278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.59
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs6069437; hg19: chr20-54444425;