2-143898268-A-G

Position:

• chr2-143898268-A-G

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 0.77 in 152,144 control chromosomes in the GnomAD database, including 45,299 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 0.77 (45299 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.675

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 = 0.944 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.770 AC: 117054 AN: 152026 Hom.: 45272 Cov.: 33

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.908

Gnomad AMR AF: 0.803

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.966

Gnomad SAS AF: 0.899

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.770 AC: 117131 AN: 152144 Hom.: 45299 Cov.: 33 AF XY: 0.772 AC XY: 57419 AN XY: 74398

Gnomad4 AFR AF: 0.763

Gnomad4 AMR AF: 0.803

Gnomad4 ASJ AF: 0.650

Gnomad4 EAS AF: 0.966

Gnomad4 SAS AF: 0.899

Gnomad4 FIN AF: 0.748

Gnomad4 NFE AF: 0.751

Gnomad4 OTH AF: 0.750

Alfa AF: 0.756 Hom.: 58358

Bravo AF: 0.773

Asia WGS AF: 0.904 AC: 3144 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	5.6
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs787151; hg19: chr2-144655836;