2-127225069-A-T

Variant names:

• chr2-127225069-A-T
• rs7567389

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 0.671 in 151,998 control chromosomes in the GnomAD database, including 34,541 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 0.67 (34541 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.643

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.883 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: 0.671 AC: 101864 AN: 151880 Hom.: 34495 Cov.: 31

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.671 AC: 101971 AN: 151998 Hom.: 34541 Cov.: 31 AF XY: 0.676 AC XY: 50206 AN XY: 74312

Gnomad4 AFR AF: 0.626

Gnomad4 AMR AF: 0.770

Gnomad4 ASJ AF: 0.682

Gnomad4 EAS AF: 0.905

Gnomad4 SAS AF: 0.600

Gnomad4 FIN AF: 0.720

Gnomad4 NFE AF: 0.657

Gnomad4 OTH AF: 0.679

Alfa AF: 0.590 Hom.: 1899

Bravo AF: 0.677

Asia WGS AF: 0.785 AC: 2724 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.17
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7567389; hg19: chr2-127982645;