rs1879553

Variant names:

• chr3-118896616-A-G
• rs1879553

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 0.0749 in 152,072 control chromosomes in the GnomAD database, including 504 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 0.075 (504 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.113
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.121 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: 0.0749 AC: 11381 AN: 151952 Hom.: 502 Cov.: 32

Gnomad AFR AF: 0.0469

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.0778

Gnomad ASJ AF: 0.0882

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.0807

Gnomad FIN AF: 0.0442

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0895

Gnomad OTH AF: 0.0790

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

GnomAD4 genome AF: 0.0749 AC: 11392 AN: 152072 Hom.: 504 Cov.: 32 AF XY: 0.0738 AC XY: 5485 AN XY: 74348

African (AFR) AF: 0.0467 AC: 1941 AN: 41548

American (AMR) AF: 0.0778 AC: 1188 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0882 AC: 305 AN: 3460

East Asian (EAS) AF: 0.129 AC: 671 AN: 5182

South Asian (SAS) AF: 0.0812 AC: 392 AN: 4828

European-Finnish (FIN) AF: 0.0442 AC: 469 AN: 10604

Middle Eastern (MID) AF: 0.113 AC: 33 AN: 292

European-Non Finnish (NFE) AF: 0.0895 AC: 6075 AN: 67860

Other (OTH) AF: 0.0801 AC: 169 AN: 2110

Alfa AF: 0.0868 Hom.: 952

Bravo AF: 0.0778

Asia WGS AF: 0.0900 AC: 310 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.65
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs1879553; hg19: chr3-118615463;