rs6054434

Variant names:

• chr20-6662560-T-C
• rs6054434

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 0.766 in 152,144 control chromosomes in the GnomAD database, including 44,828 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 0.77 (44828 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.780
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.793 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: 0.766 AC: 116522 AN: 152026 Hom.: 44802 Cov.: 32

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.655

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.770

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

GnomAD4 genome AF: 0.766 AC: 116596 AN: 152144 Hom.: 44828 Cov.: 32 AF XY: 0.762 AC XY: 56633 AN XY: 74362

African (AFR) AF: 0.756 AC: 31375 AN: 41488

American (AMR) AF: 0.706 AC: 10789 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.747 AC: 2595 AN: 3472

East Asian (EAS) AF: 0.655 AC: 3380 AN: 5164

South Asian (SAS) AF: 0.659 AC: 3175 AN: 4818

European-Finnish (FIN) AF: 0.795 AC: 8420 AN: 10586

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.798 AC: 54292 AN: 68008

Other (OTH) AF: 0.764 AC: 1613 AN: 2112

Alfa AF: 0.773 Hom.: 49067

Bravo AF: 0.763

Asia WGS AF: 0.621 AC: 2160 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.0
DANN	Benign	0.60
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs6054434; hg19: chr20-6643207;