5-106083812-A-G

Variant names:

• chr5-106083812-A-G
• rs6894797

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 0.104 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
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.0960 AC: 3986 AN: 41526

American (AMR) AF: 0.0746 AC: 1139 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 435 AN: 3472

East Asian (EAS) AF: 0.0133 AC: 69 AN: 5188

South Asian (SAS) AF: 0.106 AC: 512 AN: 4830

European-Finnish (FIN) AF: 0.123 AC: 1301 AN: 10600

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7987 AN: 68000

Other (OTH) AF: 0.0928 AC: 196 AN: 2112

Alfa AF: 0.109 Hom.: 2292

Bravo AF: 0.0995

Asia WGS AF: 0.0650 AC: 225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.4
DANN	Benign	0.55
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs6894797; hg19: chr5-105419513;