chr2-68425448-G-A

Position:

• chr2-68425448-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 0.589 in 151,810 control chromosomes in the GnomAD database, including 27,893 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 0.59 (27893 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.21

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.87 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: 0.589 AC: 89361 AN: 151694 Hom.: 27879 Cov.: 30

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.892

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.653

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

GnomAD4 genome AF: 0.589 AC: 89401 AN: 151810 Hom.: 27893 Cov.: 30 AF XY: 0.594 AC XY: 44094 AN XY: 74184

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.731

Gnomad4 ASJ AF: 0.747

Gnomad4 EAS AF: 0.892

Gnomad4 SAS AF: 0.700

Gnomad4 FIN AF: 0.630

Gnomad4 NFE AF: 0.637

Gnomad4 OTH AF: 0.656

Alfa AF: 0.649 Hom.: 62088

Bravo AF: 0.589

Asia WGS AF: 0.791 AC: 2751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	12
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11126185; hg19: chr2-68652580; COSMIC: COSV53440231;