rs6108030

Variant names:

• chr20-7646647-G-A
• rs6108030

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 0.209 in 152,088 control chromosomes in the GnomAD database, including 3,388 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 0.21 (3388 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.223 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: 0.209 AC: 31708 AN: 151970 Hom.: 3378 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.0965

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.209 AC: 31724 AN: 152088 Hom.: 3388 Cov.: 32 AF XY: 0.207 AC XY: 15395 AN XY: 74336

African (AFR) AF: 0.204 AC: 8469 AN: 41504

American (AMR) AF: 0.168 AC: 2566 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 689 AN: 3470

East Asian (EAS) AF: 0.0965 AC: 499 AN: 5172

South Asian (SAS) AF: 0.184 AC: 885 AN: 4816

European-Finnish (FIN) AF: 0.258 AC: 2718 AN: 10554

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.226 AC: 15332 AN: 67972

Other (OTH) AF: 0.171 AC: 360 AN: 2110

Alfa AF: 0.215 Hom.: 14502

Bravo AF: 0.201

Asia WGS AF: 0.121 AC: 421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.10
DANN	Benign	0.40
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs6108030; hg19: chr20-7627294;