rs6054434

Variant names:

• chr20-6662560-T-C
• rs6054434

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.756

Gnomad4 AMR AF: 0.706

Gnomad4 ASJ AF: 0.747

Gnomad4 EAS AF: 0.655

Gnomad4 SAS AF: 0.659

Gnomad4 FIN AF: 0.795

Gnomad4 NFE AF: 0.798

Gnomad4 OTH AF: 0.764

Alfa AF: 0.776 Hom.: 32169

Bravo AF: 0.763

Asia WGS AF: 0.621 AC: 2160 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6054434; hg19: chr20-6643207;