2-14665318-G-A

Position:

• chr2-14665318-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 0.518 in 151,914 control chromosomes in the GnomAD database, including 23,566 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 0.52 (23566 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.309

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.835 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: 0.518 AC: 78621 AN: 151796 Hom.: 23505 Cov.: 32

Gnomad AFR AF: 0.842

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.518 AC: 78747 AN: 151914 Hom.: 23566 Cov.: 32 AF XY: 0.517 AC XY: 38344 AN XY: 74230

Gnomad4 AFR AF: 0.842

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.385

Gnomad4 SAS AF: 0.371

Gnomad4 FIN AF: 0.417

Gnomad4 NFE AF: 0.380

Gnomad4 OTH AF: 0.486

Alfa AF: 0.401 Hom.: 6483

Bravo AF: 0.537

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.73
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1434975; hg19: chr2-14805442;