5-18021926-G-A

Variant names:

• chr5-18021926-G-A
• rs6891956

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 0.168 in 152,004 control chromosomes in the GnomAD database, including 2,845 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 0.17 (2845 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.329
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25493 AN: 151886 Hom.: 2826 Cov.: 31

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.0660

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.0887

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0983

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.168 AC: 25560 AN: 152004 Hom.: 2845 Cov.: 31 AF XY: 0.167 AC XY: 12389 AN XY: 74322

African (AFR) AF: 0.300 AC: 12424 AN: 41404

American (AMR) AF: 0.184 AC: 2805 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0660 AC: 229 AN: 3468

East Asian (EAS) AF: 0.252 AC: 1299 AN: 5148

South Asian (SAS) AF: 0.158 AC: 761 AN: 4818

European-Finnish (FIN) AF: 0.0887 AC: 940 AN: 10598

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0983 AC: 6685 AN: 67992

Other (OTH) AF: 0.144 AC: 305 AN: 2112

Alfa AF: 0.0996 Hom.: 222

Bravo AF: 0.181

Asia WGS AF: 0.213 AC: 743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.6
DANN	Benign	0.48
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs6891956; hg19: chr5-18022035;