rs4128289

Variant names:

• chr2-118350839-A-G
• rs4128289

Your query was ambiguous. Multiple possible variants found:

• chr2-118350839-A-G
• chr2-118350839-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.622 in 151,978 control chromosomes in the GnomAD database, including 31,516 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 0.62 (31516 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.725 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: 0.622 AC: 94532 AN: 151860 Hom.: 31499 Cov.: 31

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.638

Gnomad SAS AF: 0.692

Gnomad FIN AF: 0.776

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.622 AC: 94587 AN: 151978 Hom.: 31516 Cov.: 31 AF XY: 0.623 AC XY: 46288 AN XY: 74302

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.663

Gnomad4 ASJ AF: 0.778

Gnomad4 EAS AF: 0.638

Gnomad4 SAS AF: 0.692

Gnomad4 FIN AF: 0.776

Gnomad4 NFE AF: 0.730

Gnomad4 OTH AF: 0.661

Alfa AF: 0.671 Hom.: 4252

Bravo AF: 0.604

Asia WGS AF: 0.651 AC: 2265 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	9.5
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4128289; hg19: chr2-119108415;