2-189485808-T-C

Variant names:

• chr2-189485808-T-C
• rs893407

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 0.743 in 152,168 control chromosomes in the GnomAD database, including 44,824 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 0.74 (44824 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.877 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: 0.743 AC: 112953 AN: 152050 Hom.: 44809 Cov.: 33

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.988

Gnomad AMR AF: 0.753

Gnomad ASJ AF: 0.826

Gnomad EAS AF: 0.789

Gnomad SAS AF: 0.777

Gnomad FIN AF: 0.908

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.883

Gnomad OTH AF: 0.753

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

GnomAD4 genome AF: 0.743 AC: 113013 AN: 152168 Hom.: 44824 Cov.: 33 AF XY: 0.745 AC XY: 55415 AN XY: 74408

Gnomad4 AFR AF: 0.443

Gnomad4 AMR AF: 0.753

Gnomad4 ASJ AF: 0.826

Gnomad4 EAS AF: 0.788

Gnomad4 SAS AF: 0.776

Gnomad4 FIN AF: 0.908

Gnomad4 NFE AF: 0.883

Gnomad4 OTH AF: 0.754

Alfa AF: 0.796 Hom.: 6260

Bravo AF: 0.714

Asia WGS AF: 0.741 AC: 2573 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.59
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs893407; hg19: chr2-190350534;