chr2-138843145-T-C

Variant names:

• chr2-138843145-T-C
• rs4245867

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 0.902 in 152,224 control chromosomes in the GnomAD database, including 62,084 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 0.90 (62084 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.902 AC: 137212 AN: 152106 Hom.: 62027 Cov.: 31

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.896

Gnomad AMR AF: 0.929

Gnomad ASJ AF: 0.870

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.933

Gnomad FIN AF: 0.931

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.916

Gnomad OTH AF: 0.897

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

GnomAD4 genome AF: 0.902 AC: 137324 AN: 152224 Hom.: 62084 Cov.: 31 AF XY: 0.904 AC XY: 67326 AN XY: 74444

African (AFR) AF: 0.851 AC: 35305 AN: 41506

American (AMR) AF: 0.929 AC: 14200 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.870 AC: 3019 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5170 AN: 5176

South Asian (SAS) AF: 0.933 AC: 4507 AN: 4830

European-Finnish (FIN) AF: 0.931 AC: 9877 AN: 10610

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.916 AC: 62284 AN: 68028

Other (OTH) AF: 0.897 AC: 1897 AN: 2114

Alfa AF: 0.898 Hom.: 8630

Bravo AF: 0.900

Asia WGS AF: 0.969 AC: 3368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.2
DANN	Benign	0.37
PhyloP100		0.076

Splicing

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

Other links and lift over

dbSNP: rs4245867; hg19: chr2-139600715;