chr5-106688510-A-C

Variant names:

• chr5-106688510-A-C
• rs1120322

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 0.884 in 151,782 control chromosomes in the GnomAD database, including 59,496 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 0.88 (59496 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.926 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: 0.884 AC: 134016 AN: 151664 Hom.: 59440 Cov.: 31

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.856

Gnomad AMR AF: 0.931

Gnomad ASJ AF: 0.890

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.948

Gnomad FIN AF: 0.915

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.907

Gnomad OTH AF: 0.895

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

GnomAD4 genome AF: 0.884 AC: 134132 AN: 151782 Hom.: 59496 Cov.: 31 AF XY: 0.886 AC XY: 65724 AN XY: 74160

African (AFR) AF: 0.812 AC: 33654 AN: 41436

American (AMR) AF: 0.931 AC: 14128 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.890 AC: 3085 AN: 3468

East Asian (EAS) AF: 0.878 AC: 4515 AN: 5140

South Asian (SAS) AF: 0.949 AC: 4582 AN: 4828

European-Finnish (FIN) AF: 0.915 AC: 9678 AN: 10576

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.907 AC: 61566 AN: 67848

Other (OTH) AF: 0.896 AC: 1888 AN: 2108

Alfa AF: 0.902 Hom.: 96379

Bravo AF: 0.878

Asia WGS AF: 0.907 AC: 3153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.9
DANN	Benign	0.52
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs1120322; hg19: chr5-106024211;