5-107804855-G-A

Variant names:

• chr5-107804855-G-A
• rs3843492

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 0.288 in 151,882 control chromosomes in the GnomAD database, including 7,193 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 0.29 (7193 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.22
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.431 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: 0.288 AC: 43743 AN: 151764 Hom.: 7180 Cov.: 31

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.0318

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.288 AC: 43791 AN: 151882 Hom.: 7193 Cov.: 31 AF XY: 0.284 AC XY: 21063 AN XY: 74256

African (AFR) AF: 0.436 AC: 18051 AN: 41354

American (AMR) AF: 0.226 AC: 3453 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 1439 AN: 3468

East Asian (EAS) AF: 0.0320 AC: 166 AN: 5180

South Asian (SAS) AF: 0.175 AC: 842 AN: 4812

European-Finnish (FIN) AF: 0.220 AC: 2327 AN: 10570

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16615 AN: 67932

Other (OTH) AF: 0.295 AC: 622 AN: 2106

Alfa AF: 0.261 Hom.: 17766

Bravo AF: 0.296

Asia WGS AF: 0.113 AC: 398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.0090
DANN	Benign	0.32
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs3843492; hg19: chr5-107140556; COSMIC: COSV53481255;