5-18867483-A-G

Variant names:

• chr5-18867483-A-G
• rs6893920

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 0.354 in 151,904 control chromosomes in the GnomAD database, including 10,946 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 0.35 (10946 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53684 AN: 151786 Hom.: 10902 Cov.: 32

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.354 AC: 53789 AN: 151904 Hom.: 10946 Cov.: 32 AF XY: 0.361 AC XY: 26816 AN XY: 74236

African (AFR) AF: 0.521 AC: 21580 AN: 41458

American (AMR) AF: 0.301 AC: 4586 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1104 AN: 3470

East Asian (EAS) AF: 0.681 AC: 3487 AN: 5124

South Asian (SAS) AF: 0.482 AC: 2326 AN: 4822

European-Finnish (FIN) AF: 0.325 AC: 3435 AN: 10570

Middle Eastern (MID) AF: 0.325 AC: 95 AN: 292

European-Non Finnish (NFE) AF: 0.239 AC: 16246 AN: 67916

Other (OTH) AF: 0.308 AC: 646 AN: 2100

Alfa AF: 0.307 Hom.: 1364

Bravo AF: 0.356

Asia WGS AF: 0.599 AC: 2079 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.9
DANN	Benign	0.80
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs6893920; hg19: chr5-18867592;