rs564053

Positions:

• chr6-94108276-A-G
• chr6-94108276-A-T

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 0.819 in 151,716 control chromosomes in the GnomAD database, including 51,071 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 0.82 (51071 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.919 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.819 AC: 124116 AN: 151598 Hom.: 51011 Cov.: 30

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.850

Gnomad ASJ AF: 0.794

Gnomad EAS AF: 0.941

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.892

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.782

Gnomad OTH AF: 0.794

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

GnomAD4 genome AF: 0.819 AC: 124236 AN: 151716 Hom.: 51071 Cov.: 30 AF XY: 0.827 AC XY: 61306 AN XY: 74118

Gnomad4 AFR AF: 0.838

Gnomad4 AMR AF: 0.850

Gnomad4 ASJ AF: 0.794

Gnomad4 EAS AF: 0.941

Gnomad4 SAS AF: 0.796

Gnomad4 FIN AF: 0.892

Gnomad4 NFE AF: 0.782

Gnomad4 OTH AF: 0.796

Alfa AF: 0.795 Hom.: 12549

Bravo AF: 0.818

Asia WGS AF: 0.826 AC: 2870 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.31
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs564053; hg19: chr6-94817994;