rs6072343

Variant names:

• chr20-41339548-G-A
• rs6072343

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 0.121 in 152,118 control chromosomes in the GnomAD database, including 1,288 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 0.12 (1288 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126
• Publications: 21 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.14 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: 0.121 AC: 18448 AN: 152000 Hom.: 1288 Cov.: 32

Gnomad AFR AF: 0.0899

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.0885

Gnomad EAS AF: 0.00366

Gnomad SAS AF: 0.0383

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.121 AC: 18461 AN: 152118 Hom.: 1288 Cov.: 32 AF XY: 0.122 AC XY: 9075 AN XY: 74374

African (AFR) AF: 0.0898 AC: 3729 AN: 41510

American (AMR) AF: 0.113 AC: 1722 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0885 AC: 307 AN: 3470

East Asian (EAS) AF: 0.00367 AC: 19 AN: 5178

South Asian (SAS) AF: 0.0388 AC: 187 AN: 4824

European-Finnish (FIN) AF: 0.230 AC: 2429 AN: 10556

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9696 AN: 67986

Other (OTH) AF: 0.114 AC: 240 AN: 2106

Alfa AF: 0.133 Hom.: 4755

Bravo AF: 0.112

Asia WGS AF: 0.0290 AC: 99 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.0
DANN	Benign	0.62
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs6072343; hg19: chr20-39968188;