rs6894797

Variant names:

• chr5-106083812-A-G
• rs6894797

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 0.104 in 152,208 control chromosomes in the GnomAD database, including 858 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 0.10 (858 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.115 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: 0.104 AC: 15754 AN: 152090 Hom.: 859 Cov.: 32

Gnomad AFR AF: 0.0961

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.0747

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.0135

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.0933

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

GnomAD4 genome AF: 0.104 AC: 15758 AN: 152208 Hom.: 858 Cov.: 32 AF XY: 0.103 AC XY: 7654 AN XY: 74414

Gnomad4 AFR AF: 0.0960

Gnomad4 AMR AF: 0.0746

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.0133

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.0928

Alfa AF: 0.110 Hom.: 388

Bravo AF: 0.0995

Asia WGS AF: 0.0650 AC: 225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.4
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6894797; hg19: chr5-105419513;