20-48491735-T-C

Variant names:

• chr20-48491735-T-C
• rs6125345

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 0.168 in 151,968 control chromosomes in the GnomAD database, including 2,617 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 0.17 (2617 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.346 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: 0.168 AC: 25566 AN: 151850 Hom.: 2617 Cov.: 31

Gnomad AFR AF: 0.0761

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.168 AC: 25561 AN: 151968 Hom.: 2617 Cov.: 31 AF XY: 0.168 AC XY: 12472 AN XY: 74280

African (AFR) AF: 0.0759 AC: 3147 AN: 41464

American (AMR) AF: 0.161 AC: 2460 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 654 AN: 3462

East Asian (EAS) AF: 0.286 AC: 1473 AN: 5154

South Asian (SAS) AF: 0.360 AC: 1732 AN: 4808

European-Finnish (FIN) AF: 0.115 AC: 1212 AN: 10570

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14224 AN: 67934

Other (OTH) AF: 0.189 AC: 398 AN: 2106

Alfa AF: 0.199 Hom.: 13350

Bravo AF: 0.164

Asia WGS AF: 0.266 AC: 925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.27
DANN	Benign	0.30
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs6125345; hg19: chr20-47119981;