rs4867917

Variant names:

• chr5-170111184-A-G
• rs4867917

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 0.544 in 151,754 control chromosomes in the GnomAD database, including 23,958 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 0.54 (23958 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.67
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.649 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: 0.545 AC: 82604 AN: 151634 Hom.: 23952 Cov.: 30

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.650

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.544 AC: 82630 AN: 151754 Hom.: 23958 Cov.: 30 AF XY: 0.543 AC XY: 40299 AN XY: 74162

African (AFR) AF: 0.336 AC: 13887 AN: 41334

American (AMR) AF: 0.633 AC: 9669 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.676 AC: 2344 AN: 3468

East Asian (EAS) AF: 0.469 AC: 2402 AN: 5122

South Asian (SAS) AF: 0.668 AC: 3201 AN: 4790

European-Finnish (FIN) AF: 0.526 AC: 5539 AN: 10522

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.644 AC: 43723 AN: 67926

Other (OTH) AF: 0.562 AC: 1186 AN: 2110

Alfa AF: 0.573 Hom.: 4925

Bravo AF: 0.541

Asia WGS AF: 0.563 AC: 1957 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.2
DANN	Benign	0.85
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs4867917; hg19: chr5-169538188;