rs6097170

Variant names:

• chr20-52952411-A-G
• rs6097170

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 0.154 in 152,006 control chromosomes in the GnomAD database, including 2,079 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 0.15 (2079 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23421 AN: 151888 Hom.: 2077 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0828

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.0954

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.154 AC: 23455 AN: 152006 Hom.: 2079 Cov.: 32 AF XY: 0.152 AC XY: 11324 AN XY: 74320

African (AFR) AF: 0.245 AC: 10133 AN: 41442

American (AMR) AF: 0.114 AC: 1744 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 440 AN: 3466

East Asian (EAS) AF: 0.0828 AC: 429 AN: 5180

South Asian (SAS) AF: 0.168 AC: 806 AN: 4808

European-Finnish (FIN) AF: 0.0954 AC: 1009 AN: 10574

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

European-Non Finnish (NFE) AF: 0.125 AC: 8507 AN: 67962

Other (OTH) AF: 0.123 AC: 260 AN: 2108

Alfa AF: 0.128 Hom.: 2699

Bravo AF: 0.157

Asia WGS AF: 0.143 AC: 499 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.0
DANN	Benign	0.69
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs6097170; hg19: chr20-51568950;