2-216210445-T-G

Variant names:

• chr2-216210445-T-G
• rs207887

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.840 AC: 34825 AN: 41480

American (AMR) AF: 0.700 AC: 10695 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.821 AC: 2852 AN: 3472

East Asian (EAS) AF: 0.489 AC: 2526 AN: 5166

South Asian (SAS) AF: 0.857 AC: 4127 AN: 4818

European-Finnish (FIN) AF: 0.906 AC: 9595 AN: 10594

Middle Eastern (MID) AF: 0.887 AC: 259 AN: 292

European-Non Finnish (NFE) AF: 0.882 AC: 59957 AN: 68002

Other (OTH) AF: 0.808 AC: 1702 AN: 2106

Alfa AF: 0.849 Hom.: 65090

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
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs207887; hg19: chr2-217075168; COSMIC: COSV107495099;