20-6645571-G-A

Variant names:

• chr20-6645571-G-A
• rs2145272

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 0.667 in 151,978 control chromosomes in the GnomAD database, including 34,003 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 0.67 (34003 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.552
• Publications: 43 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 (EAS) allele frequency at 95% confidence interval = 0.873 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: 0.666 AC: 101199 AN: 151860 Hom.: 33955 Cov.: 31

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.751

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.894

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.667 AC: 101304 AN: 151978 Hom.: 34003 Cov.: 31 AF XY: 0.669 AC XY: 49720 AN XY: 74270

African (AFR) AF: 0.651 AC: 26978 AN: 41456

American (AMR) AF: 0.752 AC: 11475 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1973 AN: 3466

East Asian (EAS) AF: 0.894 AC: 4612 AN: 5158

South Asian (SAS) AF: 0.553 AC: 2667 AN: 4820

European-Finnish (FIN) AF: 0.718 AC: 7575 AN: 10556

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.645 AC: 43833 AN: 67948

Other (OTH) AF: 0.662 AC: 1399 AN: 2114

Alfa AF: 0.649 Hom.: 5759

Bravo AF: 0.671

Asia WGS AF: 0.697 AC: 2427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.27
DANN	Benign	0.44
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs2145272; hg19: chr20-6626218;