rs2119888

Variant names:

• chr4-99458991-A-G
• rs2119888

Your query was ambiguous. Multiple possible variants found:

• chr4-99458991-A-G
• chr4-99458991-A-T

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 0.399 in 152,028 control chromosomes in the GnomAD database, including 13,583 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 0.40 (13583 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.182
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.489 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: 0.399 AC: 60564 AN: 151910 Hom.: 13578 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.399 AC: 60605 AN: 152028 Hom.: 13583 Cov.: 32 AF XY: 0.403 AC XY: 29913 AN XY: 74304

African (AFR) AF: 0.194 AC: 8041 AN: 41482

American (AMR) AF: 0.475 AC: 7253 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1567 AN: 3470

East Asian (EAS) AF: 0.270 AC: 1393 AN: 5162

South Asian (SAS) AF: 0.371 AC: 1782 AN: 4806

European-Finnish (FIN) AF: 0.521 AC: 5507 AN: 10574

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.494 AC: 33560 AN: 67956

Other (OTH) AF: 0.416 AC: 874 AN: 2100

Alfa AF: 0.472 Hom.: 30316

Bravo AF: 0.390

Asia WGS AF: 0.357 AC: 1244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	8.0
DANN	Benign	0.91
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs2119888; hg19: chr4-100380148;