rs6870006

Variant names:

• chr5-18469349-T-A
• rs6870006

Your query was ambiguous. Multiple possible variants found:

• chr5-18469349-T-A
• chr5-18469349-T-G

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 0.73 in 151,996 control chromosomes in the GnomAD database, including 41,702 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 0.73 (41702 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.142
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.817 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: 0.731 AC: 110990 AN: 151878 Hom.: 41695 Cov.: 31

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.830

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.730 AC: 111022 AN: 151996 Hom.: 41702 Cov.: 31 AF XY: 0.731 AC XY: 54338 AN XY: 74312

African (AFR) AF: 0.591 AC: 24458 AN: 41406

American (AMR) AF: 0.611 AC: 9344 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.796 AC: 2762 AN: 3470

East Asian (EAS) AF: 0.531 AC: 2740 AN: 5164

South Asian (SAS) AF: 0.830 AC: 4003 AN: 4822

European-Finnish (FIN) AF: 0.868 AC: 9189 AN: 10582

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.823 AC: 55912 AN: 67946

Other (OTH) AF: 0.735 AC: 1556 AN: 2116

Alfa AF: 0.766 Hom.: 5683

Bravo AF: 0.699

Asia WGS AF: 0.640 AC: 2225 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.8
DANN	Benign	0.36
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs6870006; hg19: chr5-18469458;