rs6870564

chr5-17002976-A-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 0.804 in 151,792 control chromosomes in the GnomAD database, including 49,836 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 0.80 (49836 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.455

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.862 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.804 AC: 121907 AN: 151674 Hom.: 49794 Cov.: 29

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.868

Gnomad AMR AF: 0.874

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.837

Gnomad SAS AF: 0.834

Gnomad FIN AF: 0.913

Gnomad MID AF: 0.846

Gnomad NFE AF: 0.859

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.804 AC: 122005 AN: 151792 Hom.: 49836 Cov.: 29 AF XY: 0.808 AC XY: 59929 AN XY: 74180

Gnomad4 AFR AF: 0.648

Gnomad4 AMR AF: 0.874

Gnomad4 ASJ AF: 0.799

Gnomad4 EAS AF: 0.837

Gnomad4 SAS AF: 0.835

Gnomad4 FIN AF: 0.913

Gnomad4 NFE AF: 0.859

Gnomad4 OTH AF: 0.827

Alfa AF: 0.846 Hom.: 81244

Bravo AF: 0.794

Asia WGS AF: 0.823 AC: 2865 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.5
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6870564; hg19: chr5-17003085;