rs6869417

Variant names:

• chr5-31020394-T-G
• rs6869417

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 0.784 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
• Publications: 2 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 (AFR) allele frequency at 95% confidence interval = 0.842 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: 0.784 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

African (AFR) AF: 0.850 AC: 35251 AN: 41480

American (AMR) AF: 0.731 AC: 11166 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.752 AC: 2602 AN: 3462

East Asian (EAS) AF: 0.535 AC: 2759 AN: 5160

South Asian (SAS) AF: 0.577 AC: 2778 AN: 4818

European-Finnish (FIN) AF: 0.783 AC: 8281 AN: 10576

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.790 AC: 53720 AN: 67988

Other (OTH) AF: 0.779 AC: 1648 AN: 2116

Alfa AF: 0.784 Hom.: 183373

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
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs6869417; hg19: chr5-31020501;