rs6869417

Positions:

• chr5-31020394-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 0.784 in 152,088 control chromosomes in the GnomAD database, including 47,228 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 0.78 (47228 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.575

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 (AFR) allele frequency at 95% confidence interval = 0.842 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: 0.784 AC: 119093 AN: 151970 Hom.: 47187 Cov.: 32

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.849

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.784 AC: 119197 AN: 152088 Hom.: 47228 Cov.: 32 AF XY: 0.778 AC XY: 57834 AN XY: 74346

Gnomad4 AFR AF: 0.850

Gnomad4 AMR AF: 0.731

Gnomad4 ASJ AF: 0.752

Gnomad4 EAS AF: 0.535

Gnomad4 SAS AF: 0.577

Gnomad4 FIN AF: 0.783

Gnomad4 NFE AF: 0.790

Gnomad4 OTH AF: 0.779

Alfa AF: 0.782 Hom.: 84683

Bravo AF: 0.784

Asia WGS AF: 0.575 AC: 2000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.97
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6869417; hg19: chr5-31020501;