rs6867021

Variant names:

• chr5-79933823-A-G
• rs6867021
• XR_948500.3:n.198+37664A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_948500.3(LOC105379048):​n.198+37664A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.633 in 152,136 control chromosomes in the GnomAD database, including 30,577 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 0.63 (30577 hom., cov: 33)
• Consequence: LOC105379048 XR_948500.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01
• Publications: 2 publications found

Genes affected

LOC105379048 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.688 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: 0.633 AC: 96295 AN: 152018 Hom.: 30561 Cov.: 33

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.633 AC: 96363 AN: 152136 Hom.: 30577 Cov.: 33 AF XY: 0.632 AC XY: 46984 AN XY: 74380

African (AFR) AF: 0.695 AC: 28826 AN: 41486

American (AMR) AF: 0.636 AC: 9720 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.705 AC: 2445 AN: 3470

East Asian (EAS) AF: 0.565 AC: 2927 AN: 5176

South Asian (SAS) AF: 0.560 AC: 2701 AN: 4824

European-Finnish (FIN) AF: 0.594 AC: 6284 AN: 10574

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.606 AC: 41231 AN: 68002

Other (OTH) AF: 0.643 AC: 1359 AN: 2112

Alfa AF: 0.628 Hom.: 4706

Bravo AF: 0.642

Asia WGS AF: 0.604 AC: 2101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	14
DANN	Benign	0.83
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs6867021; hg19: chr5-79229646;