chr2-215929301-C-T

Variant names:

• chr2-215929301-C-T
• rs4674039

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 0.319 in 151,802 control chromosomes in the GnomAD database, including 8,579 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 0.32 (8579 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.610

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48361 AN: 151680 Hom.: 8549 Cov.: 31

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.319 AC: 48439 AN: 151802 Hom.: 8579 Cov.: 31 AF XY: 0.325 AC XY: 24121 AN XY: 74154

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.384

Gnomad4 ASJ AF: 0.280

Gnomad4 EAS AF: 0.727

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.341

Alfa AF: 0.277 Hom.: 12686

Bravo AF: 0.338

Asia WGS AF: 0.565 AC: 1963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.27
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4674039; hg19: chr2-216794024;