2-216210445-T-G

Variant names:

• chr2-216210445-T-G
• rs207887

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 0.837 in 152,122 control chromosomes in the GnomAD database, including 53,992 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 0.84 (53992 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.642

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 (NFE) allele frequency at 95% confidence interval = 0.876 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: 0.837 AC: 127280 AN: 152002 Hom.: 53940 Cov.: 31

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.928

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.821

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.856

Gnomad FIN AF: 0.906

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.882

Gnomad OTH AF: 0.810

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

GnomAD4 genome AF: 0.837 AC: 127384 AN: 152122 Hom.: 53992 Cov.: 31 AF XY: 0.834 AC XY: 61986 AN XY: 74356

Gnomad4 AFR AF: 0.840

Gnomad4 AMR AF: 0.700

Gnomad4 ASJ AF: 0.821

Gnomad4 EAS AF: 0.489

Gnomad4 SAS AF: 0.857

Gnomad4 FIN AF: 0.906

Gnomad4 NFE AF: 0.882

Gnomad4 OTH AF: 0.808

Alfa AF: 0.852 Hom.: 49080

Bravo AF: 0.817

Asia WGS AF: 0.699 AC: 2433 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	5.1
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs207887; hg19: chr2-217075168;