2-189485808-T-C

Variant names:

• chr2-189485808-T-C
• rs893407

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 0.743 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
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• 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

African (AFR) AF: 0.443 AC: 18384 AN: 41460

American (AMR) AF: 0.753 AC: 11513 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.826 AC: 2865 AN: 3470

East Asian (EAS) AF: 0.788 AC: 4081 AN: 5178

South Asian (SAS) AF: 0.776 AC: 3745 AN: 4824

European-Finnish (FIN) AF: 0.908 AC: 9636 AN: 10608

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.883 AC: 60074 AN: 68024

Other (OTH) AF: 0.754 AC: 1590 AN: 2110

Alfa AF: 0.781 Hom.: 6347

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
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs893407; hg19: chr2-190350534;