rs6867384

Variant names:

• chr5-18021861-C-G
• rs6867384

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 0.169 in 151,976 control chromosomes in the GnomAD database, including 2,862 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 (2862 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300
• Publications: 4 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 = 0.297 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: 0.168 AC: 25553 AN: 151858 Hom.: 2843 Cov.: 31

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.0912

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.0660

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.0888

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0985

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.169 AC: 25620 AN: 151976 Hom.: 2862 Cov.: 31 AF XY: 0.167 AC XY: 12421 AN XY: 74278

African (AFR) AF: 0.301 AC: 12466 AN: 41422

American (AMR) AF: 0.184 AC: 2813 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0660 AC: 229 AN: 3470

East Asian (EAS) AF: 0.253 AC: 1300 AN: 5130

South Asian (SAS) AF: 0.158 AC: 760 AN: 4814

European-Finnish (FIN) AF: 0.0888 AC: 938 AN: 10566

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

European-Non Finnish (NFE) AF: 0.0985 AC: 6698 AN: 67988

Other (OTH) AF: 0.144 AC: 304 AN: 2108

Alfa AF: 0.139 Hom.: 221

Bravo AF: 0.181

Asia WGS AF: 0.213 AC: 743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.40
PhyloP100		0.0030

Splicing

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

Other links and lift over

dbSNP: rs6867384; hg19: chr5-18021970;