chr2-44902376-G-A

Position:

• chr2-44902376-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 0.369 in 152,078 control chromosomes in the GnomAD database, including 14,037 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 0.37 (14037 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.303

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.707 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: 0.368 AC: 55981 AN: 151960 Hom.: 14003 Cov.: 32

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.369 AC: 56066 AN: 152078 Hom.: 14037 Cov.: 32 AF XY: 0.368 AC XY: 27326 AN XY: 74322

Gnomad4 AFR AF: 0.713

Gnomad4 AMR AF: 0.378

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.261

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.316

Alfa AF: 0.252 Hom.: 4617

Bravo AF: 0.397

Asia WGS AF: 0.312 AC: 1086 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1470524; hg19: chr2-45129515;