chr2-228360409-C-T

Position:

• chr2-228360409-C-T

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 0.185 in 151,972 control chromosomes in the GnomAD database, including 3,063 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 0.18 (3063 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.671

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 = 0.292 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: 0.185 AC: 28062 AN: 151856 Hom.: 3055 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.0865

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.185 AC: 28100 AN: 151972 Hom.: 3063 Cov.: 32 AF XY: 0.186 AC XY: 13796 AN XY: 74268

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.0865

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.165

Alfa AF: 0.169 Hom.: 282

Bravo AF: 0.185

Asia WGS AF: 0.136 AC: 472 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.0
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6724689; hg19: chr2-229225125;