chr2-118350839-A-G

Variant names:

• chr2-118350839-A-G
• rs4128289

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 0.622 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
• Publications: 2 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 (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

African (AFR) AF: 0.365 AC: 15139 AN: 41420

American (AMR) AF: 0.663 AC: 10105 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.778 AC: 2701 AN: 3470

East Asian (EAS) AF: 0.638 AC: 3308 AN: 5184

South Asian (SAS) AF: 0.692 AC: 3329 AN: 4812

European-Finnish (FIN) AF: 0.776 AC: 8188 AN: 10556

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.730 AC: 49628 AN: 67974

Other (OTH) AF: 0.661 AC: 1393 AN: 2106

Alfa AF: 0.659 Hom.: 4315

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
PhyloP100		-0.0050

Splicing

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

Other links and lift over

dbSNP: rs4128289; hg19: chr2-119108415;