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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.731 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

Gnomad4 AFR AF: 0.591

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.796

Gnomad4 EAS AF: 0.531

Gnomad4 SAS AF: 0.830

Gnomad4 FIN AF: 0.868

Gnomad4 NFE AF: 0.823

Gnomad4 OTH AF: 0.735

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6870006; hg19: chr5-18469458;