2-189485808-T-C

Position:

• chr2-189485808-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;