20-6610469-A-G

Variant names:

• chr20-6610469-A-G
• rs6107848

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The variant allele was found at a frequency of 0.626 in 152,000 control chromosomes in the GnomAD database, including 30,359 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 0.63 (30359 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.58
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.17).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.817 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: 0.626 AC: 95108 AN: 151882 Hom.: 30324 Cov.: 31

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.838

Gnomad SAS AF: 0.550

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.626 AC: 95191 AN: 152000 Hom.: 30359 Cov.: 31 AF XY: 0.630 AC XY: 46831 AN XY: 74288

African (AFR) AF: 0.536 AC: 22180 AN: 41418

American (AMR) AF: 0.744 AC: 11366 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1961 AN: 3466

East Asian (EAS) AF: 0.838 AC: 4335 AN: 5174

South Asian (SAS) AF: 0.549 AC: 2641 AN: 4812

European-Finnish (FIN) AF: 0.713 AC: 7533 AN: 10562

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 43029 AN: 67980

Other (OTH) AF: 0.616 AC: 1303 AN: 2114

Alfa AF: 0.589 Hom.: 10791

Bravo AF: 0.627

Asia WGS AF: 0.677 AC: 2356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.17
CADD	Benign	18
DANN	Benign	0.75
PhyloP100		3.6

Splicing

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

Other links and lift over

dbSNP: rs6107848; hg19: chr20-6591116;