rs1899169

Variant names:

• chr3-166177080-G-A
• rs1899169

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 0.485 in 151,696 control chromosomes in the GnomAD database, including 19,475 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 0.49 (19475 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.349
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.607 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: 0.485 AC: 73563 AN: 151578 Hom.: 19470 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.485 AC: 73600 AN: 151696 Hom.: 19475 Cov.: 32 AF XY: 0.489 AC XY: 36237 AN XY: 74108

African (AFR) AF: 0.262 AC: 10873 AN: 41438

American (AMR) AF: 0.539 AC: 8215 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1403 AN: 3464

East Asian (EAS) AF: 0.605 AC: 3073 AN: 5078

South Asian (SAS) AF: 0.625 AC: 3006 AN: 4808

European-Finnish (FIN) AF: 0.627 AC: 6626 AN: 10576

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.573 AC: 38874 AN: 67790

Other (OTH) AF: 0.463 AC: 976 AN: 2108

Alfa AF: 0.535 Hom.: 28847

Bravo AF: 0.467

Asia WGS AF: 0.608 AC: 2110 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.76
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs1899169; hg19: chr3-165894868;