chr6-94108276-A-G

Variant names:

• chr6-94108276-A-G
• rs564053

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;