rs4128289

chr2-118350839-A-Gchr2-118350839-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;