20-6251236-T-A

Variant names:

• chr20-6251236-T-A
• rs10485704

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 0.191 in 151,882 control chromosomes in the GnomAD database, including 3,051 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 0.19 (3051 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.266 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: 0.191 AC: 29031 AN: 151764 Hom.: 3041 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.0949

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.191 AC: 29059 AN: 151882 Hom.: 3051 Cov.: 32 AF XY: 0.193 AC XY: 14322 AN XY: 74230

African (AFR) AF: 0.271 AC: 11203 AN: 41408

American (AMR) AF: 0.192 AC: 2931 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 655 AN: 3462

East Asian (EAS) AF: 0.114 AC: 589 AN: 5156

South Asian (SAS) AF: 0.227 AC: 1095 AN: 4814

European-Finnish (FIN) AF: 0.163 AC: 1716 AN: 10550

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10360 AN: 67924

Other (OTH) AF: 0.180 AC: 378 AN: 2104

Alfa AF: 0.155 Hom.: 249

Bravo AF: 0.194

Asia WGS AF: 0.154 AC: 537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.4
DANN	Benign	0.77
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs10485704; hg19: chr20-6231883;