2-138843145-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

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

Gnomad4 AFR AF: 0.851 AC: 0.8506 AN: 0.8506

Gnomad4 AMR AF: 0.929 AC: 0.928955 AN: 0.928955

Gnomad4 ASJ AF: 0.870 AC: 0.869528 AN: 0.869528

Gnomad4 EAS AF: 0.999 AC: 0.998841 AN: 0.998841

Gnomad4 SAS AF: 0.933 AC: 0.933126 AN: 0.933126

Gnomad4 FIN AF: 0.931 AC: 0.930914 AN: 0.930914

Gnomad4 NFE AF: 0.916 AC: 0.915564 AN: 0.915564

Gnomad4 OTH AF: 0.897 AC: 0.897351 AN: 0.897351

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4245867; hg19: chr2-139600715;