2-14661789-G-A

Position:

• chr2-14661789-G-A

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 0.513 in 151,536 control chromosomes in the GnomAD database, including 23,235 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 0.51 (23235 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.841 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: 0.513 AC: 77620 AN: 151418 Hom.: 23178 Cov.: 30

Gnomad AFR AF: 0.848

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.513 AC: 77743 AN: 151536 Hom.: 23235 Cov.: 30 AF XY: 0.511 AC XY: 37824 AN XY: 74002

Gnomad4 AFR AF: 0.848

Gnomad4 AMR AF: 0.439

Gnomad4 ASJ AF: 0.349

Gnomad4 EAS AF: 0.352

Gnomad4 SAS AF: 0.404

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.376

Gnomad4 OTH AF: 0.478

Alfa AF: 0.260 Hom.: 519

Bravo AF: 0.536

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	2.8
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7602960; hg19: chr2-14801913;