rs1914516

Variant names:

• chr2-214697209-T-C
• rs1914516

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 0.786 in 152,194 control chromosomes in the GnomAD database, including 47,114 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 0.79 (47114 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.815 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: 0.786 AC: 119474 AN: 152074 Hom.: 47078 Cov.: 32

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.716

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.749

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

GnomAD4 genome AF: 0.786 AC: 119563 AN: 152194 Hom.: 47114 Cov.: 32 AF XY: 0.792 AC XY: 58945 AN XY: 74402

Gnomad4 AFR AF: 0.788

Gnomad4 AMR AF: 0.813

Gnomad4 ASJ AF: 0.716

Gnomad4 EAS AF: 0.760

Gnomad4 SAS AF: 0.836

Gnomad4 FIN AF: 0.871

Gnomad4 NFE AF: 0.769

Gnomad4 OTH AF: 0.752

Alfa AF: 0.786 Hom.: 7934

Bravo AF: 0.778

Asia WGS AF: 0.807 AC: 2806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1914516; hg19: chr2-215561933;