chr2-219578794-T-C

Position:

• chr2-219578794-T-C

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 0.494 in 152,016 control chromosomes in the GnomAD database, including 18,817 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 0.49 (18817 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.715

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.561 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: 0.494 AC: 75026 AN: 151898 Hom.: 18812 Cov.: 32

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.494 AC: 75070 AN: 152016 Hom.: 18817 Cov.: 32 AF XY: 0.494 AC XY: 36718 AN XY: 74284

Gnomad4 AFR AF: 0.502

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.506

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.579

Gnomad4 FIN AF: 0.470

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.503

Alfa AF: 0.500 Hom.: 38689

Bravo AF: 0.492

Asia WGS AF: 0.427 AC: 1489 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.2
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6729914; hg19: chr2-220443516;