chr2-120487546-T-C

Variant names:

• chr2-120487546-T-C
• rs4849887

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 0.834 in 152,146 control chromosomes in the GnomAD database, including 53,542 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 0.83 (53542 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470
• Publications: 83 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.892 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: 0.834 AC: 126811 AN: 152028 Hom.: 53528 Cov.: 32

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.945

Gnomad AMR AF: 0.869

Gnomad ASJ AF: 0.850

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.938

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.898

Gnomad OTH AF: 0.836

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

GnomAD4 genome AF: 0.834 AC: 126875 AN: 152146 Hom.: 53542 Cov.: 32 AF XY: 0.836 AC XY: 62220 AN XY: 74394

African (AFR) AF: 0.697 AC: 28923 AN: 41468

American (AMR) AF: 0.868 AC: 13281 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.850 AC: 2950 AN: 3472

East Asian (EAS) AF: 0.779 AC: 4022 AN: 5162

South Asian (SAS) AF: 0.791 AC: 3807 AN: 4810

European-Finnish (FIN) AF: 0.938 AC: 9948 AN: 10606

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.898 AC: 61078 AN: 68016

Other (OTH) AF: 0.833 AC: 1762 AN: 2114

Alfa AF: 0.869 Hom.: 106142

Bravo AF: 0.824

Asia WGS AF: 0.752 AC: 2613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.5
DANN	Benign	0.40
PhyloP100		-0.047

Splicing

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

Other links and lift over

dbSNP: rs4849887; hg19: chr2-121245122;