rs6063454

Variant names:

• chr20-49974254-G-T
• rs6063454

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 0.329 in 152,062 control chromosomes in the GnomAD database, including 9,765 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 0.33 (9765 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.258
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.534 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: 0.329 AC: 50035 AN: 151944 Hom.: 9758 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.329 AC: 50066 AN: 152062 Hom.: 9765 Cov.: 32 AF XY: 0.342 AC XY: 25397 AN XY: 74326

African (AFR) AF: 0.118 AC: 4919 AN: 41534

American (AMR) AF: 0.326 AC: 4967 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1251 AN: 3470

East Asian (EAS) AF: 0.238 AC: 1226 AN: 5154

South Asian (SAS) AF: 0.551 AC: 2652 AN: 4812

European-Finnish (FIN) AF: 0.547 AC: 5781 AN: 10576

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.415 AC: 28182 AN: 67950

Other (OTH) AF: 0.342 AC: 722 AN: 2112

Alfa AF: 0.385 Hom.: 1871

Bravo AF: 0.294

Asia WGS AF: 0.422 AC: 1468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.72
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs6063454; hg19: chr20-48590791;