rs3815854

chr2-219804017-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 0.509 in 152,078 control chromosomes in the GnomAD database, including 20,167 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 0.51 (20167 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.674 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: 0.509 AC: 77383 AN: 151960 Hom.: 20152 Cov.: 33

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.509 AC: 77440 AN: 152078 Hom.: 20167 Cov.: 33 AF XY: 0.512 AC XY: 38078 AN XY: 74374

Gnomad4 AFR AF: 0.578

Gnomad4 AMR AF: 0.532

Gnomad4 ASJ AF: 0.580

Gnomad4 EAS AF: 0.692

Gnomad4 SAS AF: 0.474

Gnomad4 FIN AF: 0.475

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.522

Alfa AF: 0.472 Hom.: 7303

Bravo AF: 0.518

Asia WGS AF: 0.545 AC: 1893 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	6.2
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3815854; hg19: chr2-220668738;